printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bedtools 2>&1 WARNING: your info file index has not been updated for 14 days. You should run 'fink selfupdate' to get the latest package descriptions. The package 'bedtools' will be built without being installed. Reading build dependency for bedtools-2.20.1-2... Reading dependency for bedtools-2.20.1-2... Reading build conflict for bedtools-2.20.1-2... The package 'setuptools-tng-py27' will be installed. Reading dependency for setuptools-tng-py27-5.1-1... Reading runtime dependency for setuptools-tng-py27-5.1-1... The package 'sphinx-py27' will be installed. Reading dependency for sphinx-py27-1.2.2-1... Reading runtime dependency for sphinx-py27-1.2.2-1... The package 'python27' will be installed. Reading dependency for python27-2.7.8-1... Reading runtime dependency for python27-2.7.8-1... The package 'jinja2-py27' will be installed. Reading dependency for jinja2-py27-2.7.3-1... Reading runtime dependency for jinja2-py27-2.7.3-1... The package 'pygments-py27' will be installed. Reading dependency for pygments-py27-1.6-2... Reading runtime dependency for pygments-py27-1.6-2... The package 'docutils-py27' will be installed. Reading dependency for docutils-py27-0.10-2... Reading runtime dependency for docutils-py27-0.10-2... The package 'python27-shlibs' will be installed. Reading dependency for python27-shlibs-2.7.8-1... Reading runtime dependency for python27-shlibs-2.7.8-1... The package 'blt-shlibs' will be installed. Reading dependency for blt-shlibs-2.4z-160... Reading runtime dependency for blt-shlibs-2.4z-160... The package 'gdbm3-shlibs' will be installed. Reading dependency for gdbm3-shlibs-1.8.3-4... Reading runtime dependency for gdbm3-shlibs-1.8.3-4... The package 'libffi6-shlibs' will be installed. Reading dependency for libffi6-shlibs-3.1-1... Reading runtime dependency for libffi6-shlibs-3.1-1... The package 'libncursesw5-shlibs' will be installed. Reading dependency for libncursesw5-shlibs-5.9-20110507-1... Reading runtime dependency for libncursesw5-shlibs-5.9-20110507-1... The package 'sqlite3-shlibs' will be installed. Reading dependency for sqlite3-shlibs-3.8.3.1-1... Reading runtime dependency for sqlite3-shlibs-3.8.3.1-1... The package 'tcltk' will be installed. Reading dependency for tcltk-8.6.1-104... Reading runtime dependency for tcltk-8.6.1-104... The package 'markupsafe-py27' will be installed. Reading dependency for markupsafe-py27-0.23-1... Reading runtime dependency for markupsafe-py27-0.23-1... The package 'libjpeg9-shlibs' will be installed. Reading dependency for libjpeg9-shlibs-9a-1... Reading runtime dependency for libjpeg9-shlibs-9a-1... The package 'tcltk-shlibs' will be installed. Reading dependency for tcltk-shlibs-8.6.1-104... Reading runtime dependency for tcltk-shlibs-8.6.1-104... The package 'fontconfig2-shlibs' will be installed. Reading dependency for fontconfig2-shlibs-2.10.2-1... Reading runtime dependency for fontconfig2-shlibs-2.10.2-1... The package 'freetype219-shlibs' will be installed. Reading dependency for freetype219-shlibs-2.4.12-1... Reading runtime dependency for freetype219-shlibs-2.4.12-1... The package 'xft2-shlibs' will be installed. Reading dependency for xft2-shlibs-2.2.0-3... Reading runtime dependency for xft2-shlibs-2.2.0-3... The package 'beaker-py27' will be installed. Reading dependency for beaker-py27-1.6.4-2... Reading runtime dependency for beaker-py27-1.6.4-2... The package 'fontconfig-config' will be installed. Reading dependency for fontconfig-config-2.10.2-1... Reading runtime dependency for fontconfig-config-2.10.2-1... The following package will be rebuilt: bedtools The following 21 additional packages will be installed: beaker-py27 blt-shlibs docutils-py27 fontconfig-config fontconfig2-shlibs freetype219-shlibs gdbm3-shlibs jinja2-py27 libffi6-shlibs libjpeg9-shlibs libncursesw5-shlibs markupsafe-py27 pygments-py27 python27 python27-shlibs setuptools-tng-py27 sphinx-py27 sqlite3-shlibs tcltk tcltk-shlibs xft2-shlibs Do you want to continue? [Y/n] (assuming default) Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/freetype219-shlibs_2.4.12-1_darwin-x86_64.deb Selecting previously deselected package freetype219-shlibs. (Reading database ... 6827 files and directories currently installed.) Unpacking freetype219-shlibs (from .../freetype219-shlibs_2.4.12-1_darwin-x86_64.deb) ... Setting up freetype219-shlibs (2.4.12-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb Selecting previously deselected package gdbm3-shlibs. (Reading database ... 6838 files and directories currently installed.) Unpacking gdbm3-shlibs (from .../gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb) ... Setting up gdbm3-shlibs (1.8.3-4) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libffi6-shlibs_3.1-1_darwin-x86_64.deb Selecting previously deselected package libffi6-shlibs. (Reading database ... 6846 files and directories currently installed.) Unpacking libffi6-shlibs (from .../libffi6-shlibs_3.1-1_darwin-x86_64.deb) ... Setting up libffi6-shlibs (3.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/libjpeg9-shlibs_9a-1_darwin-x86_64.deb Selecting previously deselected package libjpeg9-shlibs. (Reading database ... 6847 files and directories currently installed.) Unpacking libjpeg9-shlibs (from .../libjpeg9-shlibs_9a-1_darwin-x86_64.deb) ... Setting up libjpeg9-shlibs (9a-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb Selecting previously deselected package libncursesw5-shlibs. (Reading database ... 6850 files and directories currently installed.) Unpacking libncursesw5-shlibs (from .../libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb) ... Setting up libncursesw5-shlibs (5.9-20110507-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/database/sqlite3-shlibs_3.8.3.1-1_darwin-x86_64.deb Selecting previously deselected package sqlite3-shlibs. (Reading database ... 6861 files and directories currently installed.) Unpacking sqlite3-shlibs (from .../sqlite3-shlibs_3.8.3.1-1_darwin-x86_64.deb) ... Setting up sqlite3-shlibs (3.8.3.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/fontconfig2-shlibs_2.10.2-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/fontconfig-config_2.10.2-1_darwin-x86_64.deb Selecting previously deselected package fontconfig2-shlibs. (Reading database ... 6865 files and directories currently installed.) Unpacking fontconfig2-shlibs (from .../fontconfig2-shlibs_2.10.2-1_darwin-x86_64.deb) ... Selecting previously deselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.10.2-1_darwin-x86_64.deb) ... Setting up fontconfig-config (2.10.2-1) ... Setting up fontconfig2-shlibs (2.10.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/xft2-shlibs_2.2.0-3_darwin-x86_64.deb Selecting previously deselected package xft2-shlibs. (Reading database ... 6950 files and directories currently installed.) Unpacking xft2-shlibs (from .../xft2-shlibs_2.2.0-3_darwin-x86_64.deb) ... Setting up xft2-shlibs (2.2.0-3) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/tcltk_8.6.1-104_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/tcltk-shlibs_8.6.1-104_darwin-x86_64.deb Selecting previously deselected package tcltk. (Reading database ... 6959 files and directories currently installed.) Unpacking tcltk (from .../tcltk_8.6.1-104_darwin-x86_64.deb) ... Selecting previously deselected package tcltk-shlibs. Unpacking tcltk-shlibs (from .../tcltk-shlibs_8.6.1-104_darwin-x86_64.deb) ... Setting up tcltk-shlibs (8.6.1-104) ... Setting up tcltk (8.6.1-104) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/blt-shlibs_2.4z-160_darwin-x86_64.deb Selecting previously deselected package blt-shlibs. (Reading database ... 7434 files and directories currently installed.) Unpacking blt-shlibs (from .../blt-shlibs_2.4z-160_darwin-x86_64.deb) ... Setting up blt-shlibs (2.4z-160) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/python27_2.7.8-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/python27-shlibs_2.7.8-1_darwin-x86_64.deb Selecting previously deselected package python27. (Reading database ... 7440 files and directories currently installed.) Unpacking python27 (from .../python27_2.7.8-1_darwin-x86_64.deb) ... Selecting previously deselected package python27-shlibs. Unpacking python27-shlibs (from .../python27-shlibs_2.7.8-1_darwin-x86_64.deb) ... Setting up python27-shlibs (2.7.8-1) ... Setting up python27 (2.7.8-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/setuptools-tng-py27_5.1-1_darwin-x86_64.deb Selecting previously deselected package setuptools-tng-py27. (Reading database ... 14651 files and directories currently installed.) Unpacking setuptools-tng-py27 (from .../setuptools-tng-py27_5.1-1_darwin-x86_64.deb) ... Setting up setuptools-tng-py27 (5.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/beaker-py27_1.6.4-2_darwin-x86_64.deb Selecting previously deselected package beaker-py27. (Reading database ... 14822 files and directories currently installed.) Unpacking beaker-py27 (from .../beaker-py27_1.6.4-2_darwin-x86_64.deb) ... Setting up beaker-py27 (1.6.4-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/docutils-py27_0.10-2_darwin-x86_64.deb Selecting previously deselected package docutils-py27. (Reading database ... 14877 files and directories currently installed.) Unpacking docutils-py27 (from .../docutils-py27_0.10-2_darwin-x86_64.deb) ... Setting up docutils-py27 (0.10-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/markupsafe-py27_0.23-1_darwin-x86_64.deb Selecting previously deselected package markupsafe-py27. (Reading database ... 15257 files and directories currently installed.) Unpacking markupsafe-py27 (from .../markupsafe-py27_0.23-1_darwin-x86_64.deb) ... Setting up markupsafe-py27 (0.23-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/pygments-py27_1.6-2_darwin-x86_64.deb Selecting previously deselected package pygments-py27. (Reading database ... 15282 files and directories currently installed.) Unpacking pygments-py27 (from .../pygments-py27_1.6-2_darwin-x86_64.deb) ... Setting up pygments-py27 (1.6-2) ... The script 'pygmentize' installed in /sw/bin/ is a symlink automatically updated by the update-alternatives utility. If you install multiple flavors of the pygmentize package the symlinks will point to the higher flavor by default. Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/jinja2-py27_2.7.3-1_darwin-x86_64.deb Selecting previously deselected package jinja2-py27. (Reading database ... 15473 files and directories currently installed.) Unpacking jinja2-py27 (from .../jinja2-py27_2.7.3-1_darwin-x86_64.deb) ... Setting up jinja2-py27 (2.7.3-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/sphinx-py27_1.2.2-1_darwin-x86_64.deb Selecting previously deselected package sphinx-py27. (Reading database ... 15609 files and directories currently installed.) Unpacking sphinx-py27 (from .../sphinx-py27_1.2.2-1_darwin-x86_64.deb) ... Setting up sphinx-py27 (1.2.2-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bedtools-2.20.1-2 /sw/build.build dpkg-deb: building package `fink-buildlock-bedtools-2.20.1-2' in `/sw/build.build/fink-buildlock-bedtools-2.20.1-2_2014.08.07-22.59.22_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bedtools-2.20.1-2_2014.08.07-22.59.22_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bedtools-2.20.1-2. (Reading database ... 16278 files and directories currently installed.) Unpacking fink-buildlock-bedtools-2.20.1-2 (from .../fink-buildlock-bedtools-2.20.1-2_2014.08.07-22.59.22_darwin-x86_64.deb) ... Setting up fink-buildlock-bedtools-2.20.1-2 (2014.08.07-22.59.22) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.mUiMc env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/bedtools-2.20.1.tar.gz bedtools2-2.20.1/ bedtools2-2.20.1/.travis.yml bedtools2-2.20.1/bin/ bedtools2-2.20.1/data/ bedtools2-2.20.1/docs/ bedtools2-2.20.1/genomes/ bedtools2-2.20.1/LICENSE bedtools2-2.20.1/Makefile bedtools2-2.20.1/obj/ bedtools2-2.20.1/README.md bedtools2-2.20.1/RELEASE_HISTORY bedtools2-2.20.1/scripts/ bedtools2-2.20.1/src/ bedtools2-2.20.1/test/ bedtools2-2.20.1/test/bamtobed/ bedtools2-2.20.1/test/bed12tobed6/ bedtools2-2.20.1/test/closest/ bedtools2-2.20.1/test/cluster/ bedtools2-2.20.1/test/coverage/ bedtools2-2.20.1/test/expand/ bedtools2-2.20.1/test/flank/ bedtools2-2.20.1/test/general/ bedtools2-2.20.1/test/genomecov/ bedtools2-2.20.1/test/getfasta/ bedtools2-2.20.1/test/groupBy/ bedtools2-2.20.1/test/intersect/ bedtools2-2.20.1/test/jaccard/ bedtools2-2.20.1/test/map/ bedtools2-2.20.1/test/merge/ bedtools2-2.20.1/test/multicov/ bedtools2-2.20.1/test/reldist/ bedtools2-2.20.1/test/sample/ bedtools2-2.20.1/test/shuffle/ bedtools2-2.20.1/test/slop/ bedtools2-2.20.1/test/subtract/ bedtools2-2.20.1/test/test.sh bedtools2-2.20.1/test/subtract/a.bed bedtools2-2.20.1/test/subtract/b.bed bedtools2-2.20.1/test/subtract/c.bed bedtools2-2.20.1/test/subtract/d.bed bedtools2-2.20.1/test/subtract/test-subtract.sh bedtools2-2.20.1/test/slop/a.bed bedtools2-2.20.1/test/slop/test-slop.sh bedtools2-2.20.1/test/slop/tiny.genome bedtools2-2.20.1/test/shuffle/excl.bed bedtools2-2.20.1/test/shuffle/incl.bed bedtools2-2.20.1/test/shuffle/simrep.bed bedtools2-2.20.1/test/shuffle/test-shuffle.sh bedtools2-2.20.1/test/sample/human.hg19.genome bedtools2-2.20.1/test/sample/sample_help_withoutVersion.txt bedtools2-2.20.1/test/sample/test-sample.sh bedtools2-2.20.1/test/reldist/test-reldist.sh bedtools2-2.20.1/test/multicov/multicov.bed bedtools2-2.20.1/test/multicov/one_block.bam.bai bedtools2-2.20.1/test/multicov/one_block.sam bedtools2-2.20.1/test/multicov/test-multicov.sh bedtools2-2.20.1/test/multicov/two_blocks.bam.bai bedtools2-2.20.1/test/multicov/two_blocks.sam bedtools2-2.20.1/test/merge/a.bed bedtools2-2.20.1/test/merge/a.full.bam bedtools2-2.20.1/test/merge/a.full.bed bedtools2-2.20.1/test/merge/a.gff bedtools2-2.20.1/test/merge/a.names.bed bedtools2-2.20.1/test/merge/b.bed bedtools2-2.20.1/test/merge/bamCol10Collapse.txt bedtools2-2.20.1/test/merge/bamCol11Collapse.txt bedtools2-2.20.1/test/merge/bamCol1Collapse.txt bedtools2-2.20.1/test/merge/bamCol3Collapse.txt bedtools2-2.20.1/test/merge/bamCol4Mean.txt bedtools2-2.20.1/test/merge/bamCol5Mean.txt bedtools2-2.20.1/test/merge/bamCol6Collapse.txt bedtools2-2.20.1/test/merge/bamCol7Collapse.txt bedtools2-2.20.1/test/merge/bamCol8Mean.txt bedtools2-2.20.1/test/merge/bamCol9Mean.txt bedtools2-2.20.1/test/merge/fullFields.bam bedtools2-2.20.1/test/merge/mergeBugTest.bed bedtools2-2.20.1/test/merge/mixedStrands.bed bedtools2-2.20.1/test/merge/precisionTest.bed bedtools2-2.20.1/test/merge/test-merge.sh bedtools2-2.20.1/test/merge/testA.vcf bedtools2-2.20.1/test/merge/unsorted.bed bedtools2-2.20.1/test/map/a.vsorted.bed bedtools2-2.20.1/test/map/b.vsorted.bed bedtools2-2.20.1/test/map/d.bed bedtools2-2.20.1/test/map/fullFields.bam bedtools2-2.20.1/test/map/genome bedtools2-2.20.1/test/map/ivls.bed bedtools2-2.20.1/test/map/ivls2.bed bedtools2-2.20.1/test/map/t.bed bedtools2-2.20.1/test/map/test-map.sh bedtools2-2.20.1/test/map/test.gff bedtools2-2.20.1/test/map/test.vcf bedtools2-2.20.1/test/map/three_blocks_match.bed bedtools2-2.20.1/test/map/three_blocks_nomatch.bed bedtools2-2.20.1/test/map/values.bam bedtools2-2.20.1/test/map/values.bed bedtools2-2.20.1/test/map/values2.bed bedtools2-2.20.1/test/map/values3.bed bedtools2-2.20.1/test/map/values4.bed bedtools2-2.20.1/test/map/values5.bed bedtools2-2.20.1/test/jaccard/a.bam bedtools2-2.20.1/test/jaccard/a.bed bedtools2-2.20.1/test/jaccard/aMixedStrands.bed bedtools2-2.20.1/test/jaccard/b.bed bedtools2-2.20.1/test/jaccard/bMixedStrands.bed bedtools2-2.20.1/test/jaccard/c.bed bedtools2-2.20.1/test/jaccard/d.bed bedtools2-2.20.1/test/jaccard/e.bed bedtools2-2.20.1/test/jaccard/test-jaccard.sh bedtools2-2.20.1/test/jaccard/three_blocks_match.bam bedtools2-2.20.1/test/jaccard/three_blocks_match.bed bedtools2-2.20.1/test/intersect/a.bam bedtools2-2.20.1/test/intersect/a.bed bedtools2-2.20.1/test/intersect/a_bgzipped.bed.gz bedtools2-2.20.1/test/intersect/a_gzipped.bed.gz bedtools2-2.20.1/test/intersect/a_with_bothUnmapped.bam bedtools2-2.20.1/test/intersect/a_withLargeHeader.bed bedtools2-2.20.1/test/intersect/a_withLargeHeader_bgzipped.bed.gz bedtools2-2.20.1/test/intersect/a_withLargeHeader_gzipped.bed.gz bedtools2-2.20.1/test/intersect/aVSb.bam bedtools2-2.20.1/test/intersect/aWithHeaderVsB.txt bedtools2-2.20.1/test/intersect/b.bed bedtools2-2.20.1/test/intersect/bed3.bed bedtools2-2.20.1/test/intersect/bed4.bed bedtools2-2.20.1/test/intersect/bed5.bed bedtools2-2.20.1/test/intersect/bed6.bed bedtools2-2.20.1/test/intersect/bed6.strand.bed bedtools2-2.20.1/test/intersect/bed6.strand2.bed bedtools2-2.20.1/test/intersect/bedplus.bed bedtools2-2.20.1/test/intersect/c.bed bedtools2-2.20.1/test/intersect/chromOrderA.bed bedtools2-2.20.1/test/intersect/chromOrderB.bed bedtools2-2.20.1/test/intersect/chromsOutOfOrder.bed bedtools2-2.20.1/test/intersect/d.bed bedtools2-2.20.1/test/intersect/dosLineChar_a.bed bedtools2-2.20.1/test/intersect/dosLineCharWithExtraTab_b.bed bedtools2-2.20.1/test/intersect/gdc.bam bedtools2-2.20.1/test/intersect/gdc.gff bedtools2-2.20.1/test/intersect/gdc_exp bedtools2-2.20.1/test/intersect/gdc_one.bed bedtools2-2.20.1/test/intersect/headerOnly.vcf bedtools2-2.20.1/test/intersect/human.hg19.genome bedtools2-2.20.1/test/intersect/human.hg19.vSort.genome bedtools2-2.20.1/test/intersect/j1.bed bedtools2-2.20.1/test/intersect/mapped_and_unmapped.sam bedtools2-2.20.1/test/intersect/new_test-intersect.sh bedtools2-2.20.1/test/intersect/one_block.sam bedtools2-2.20.1/test/intersect/oneRecordNoNewline.bed bedtools2-2.20.1/test/intersect/oneUnmapped.bam bedtools2-2.20.1/test/intersect/performanceTest.sh bedtools2-2.20.1/test/intersect/queryUnmappedMateMappedCoordsInvalid.bam bedtools2-2.20.1/test/intersect/recordsOutOfOrder.bed bedtools2-2.20.1/test/intersect/test-intersect.sh bedtools2-2.20.1/test/intersect/three_blocks.sam bedtools2-2.20.1/test/intersect/three_blocks_match.bam bedtools2-2.20.1/test/intersect/three_blocks_match.bed bedtools2-2.20.1/test/intersect/three_blocks_match_1bp.bed bedtools2-2.20.1/test/intersect/three_blocks_nomatch.bed bedtools2-2.20.1/test/intersect/two_blocks.sam bedtools2-2.20.1/test/intersect/two_blocks_partial.bam bedtools2-2.20.1/test/intersect/two_blocks_partial.bed bedtools2-2.20.1/test/groupBy/test-groupby.sh bedtools2-2.20.1/test/groupBy/values3.header.bed bedtools2-2.20.1/test/getfasta/blocks.bed bedtools2-2.20.1/test/getfasta/t.bed bedtools2-2.20.1/test/getfasta/t.fa bedtools2-2.20.1/test/getfasta/t.fa.fai bedtools2-2.20.1/test/getfasta/t_fH.fa bedtools2-2.20.1/test/getfasta/t_fH.fa.fai bedtools2-2.20.1/test/getfasta/test-getfasta.sh bedtools2-2.20.1/test/genomecov/one_block.sam bedtools2-2.20.1/test/genomecov/sam-w-del.sam bedtools2-2.20.1/test/genomecov/test-genomecov.sh bedtools2-2.20.1/test/genomecov/three_blocks.sam bedtools2-2.20.1/test/genomecov/three_blocks_match.bed bedtools2-2.20.1/test/genomecov/three_blocks_match_1bp.bed bedtools2-2.20.1/test/genomecov/three_blocks_nomatch.bed bedtools2-2.20.1/test/genomecov/two_blocks.sam bedtools2-2.20.1/test/general/c.bed bedtools2-2.20.1/test/general/c.bed.gz bedtools2-2.20.1/test/general/empty.bed bedtools2-2.20.1/test/general/exp bedtools2-2.20.1/test/general/non-empty.bed.gz bedtools2-2.20.1/test/general/obs bedtools2-2.20.1/test/general/test-general.sh bedtools2-2.20.1/test/flank/a.bed bedtools2-2.20.1/test/flank/test-flank.sh bedtools2-2.20.1/test/flank/tiny.genome bedtools2-2.20.1/test/expand/expand.txt bedtools2-2.20.1/test/expand/test-expand.sh bedtools2-2.20.1/test/coverage/one_block.bam.bai bedtools2-2.20.1/test/coverage/one_block.sam bedtools2-2.20.1/test/coverage/sam-w-del.bam.bai bedtools2-2.20.1/test/coverage/sam-w-del.sam bedtools2-2.20.1/test/coverage/test-coverage.sh bedtools2-2.20.1/test/coverage/three_blocks.bam.bai bedtools2-2.20.1/test/coverage/three_blocks.sam bedtools2-2.20.1/test/coverage/three_blocks_match.bed bedtools2-2.20.1/test/coverage/three_blocks_match_1bp.bed bedtools2-2.20.1/test/coverage/three_blocks_nomatch.bed bedtools2-2.20.1/test/coverage/two_blocks.bam.bai bedtools2-2.20.1/test/coverage/two_blocks.sam bedtools2-2.20.1/test/cluster/in.bed bedtools2-2.20.1/test/cluster/test-cluster.sh bedtools2-2.20.1/test/closest/a.bed bedtools2-2.20.1/test/closest/a.names.bed bedtools2-2.20.1/test/closest/b-one-bp-closer.bed bedtools2-2.20.1/test/closest/b.bed bedtools2-2.20.1/test/closest/b.names.bed bedtools2-2.20.1/test/closest/close-a.bed bedtools2-2.20.1/test/closest/close-b.bed bedtools2-2.20.1/test/closest/strand-test-a.bed bedtools2-2.20.1/test/closest/strand-test-b.bed bedtools2-2.20.1/test/closest/test-closest.sh bedtools2-2.20.1/test/bed12tobed6/bed6.bed bedtools2-2.20.1/test/bed12tobed6/one_blocks.bed bedtools2-2.20.1/test/bed12tobed6/test-bed12tobed6.sh bedtools2-2.20.1/test/bed12tobed6/three_blocks.bed bedtools2-2.20.1/test/bed12tobed6/two_blocks.bed bedtools2-2.20.1/test/bamtobed/one_block.sam bedtools2-2.20.1/test/bamtobed/test-bamtobed.sh bedtools2-2.20.1/test/bamtobed/three_blocks.sam bedtools2-2.20.1/test/bamtobed/two_blocks.sam bedtools2-2.20.1/test/bamtobed/two_blocks_w_D.sam bedtools2-2.20.1/src/annotateBed/ bedtools2-2.20.1/src/bamToBed/ bedtools2-2.20.1/src/bamToFastq/ bedtools2-2.20.1/src/bed12ToBed6/ bedtools2-2.20.1/src/bedpeToBam/ bedtools2-2.20.1/src/bedToBam/ bedtools2-2.20.1/src/bedToIgv/ bedtools2-2.20.1/src/bedtools.cpp bedtools2-2.20.1/src/closestBed/ bedtools2-2.20.1/src/clusterBed/ bedtools2-2.20.1/src/complementBed/ bedtools2-2.20.1/src/coverageBed/ bedtools2-2.20.1/src/expand/ bedtools2-2.20.1/src/fastaFromBed/ bedtools2-2.20.1/src/flankBed/ bedtools2-2.20.1/src/genomeCoverageBed/ bedtools2-2.20.1/src/getOverlap/ bedtools2-2.20.1/src/groupBy/ bedtools2-2.20.1/src/intersectFile/ bedtools2-2.20.1/src/jaccard/ bedtools2-2.20.1/src/linksBed/ bedtools2-2.20.1/src/mapFile/ bedtools2-2.20.1/src/maskFastaFromBed/ bedtools2-2.20.1/src/mergeFile/ bedtools2-2.20.1/src/multiBamCov/ bedtools2-2.20.1/src/multiIntersectBed/ bedtools2-2.20.1/src/nekSandbox1/ bedtools2-2.20.1/src/nucBed/ bedtools2-2.20.1/src/pairToBed/ bedtools2-2.20.1/src/pairToPair/ bedtools2-2.20.1/src/randomBed/ bedtools2-2.20.1/src/regressTest/ bedtools2-2.20.1/src/reldist/ bedtools2-2.20.1/src/sampleFile/ bedtools2-2.20.1/src/shuffleBed/ bedtools2-2.20.1/src/slopBed/ bedtools2-2.20.1/src/sortBed/ bedtools2-2.20.1/src/subtractBed/ bedtools2-2.20.1/src/tagBam/ bedtools2-2.20.1/src/unionBedGraphs/ bedtools2-2.20.1/src/utils/ bedtools2-2.20.1/src/windowBed/ bedtools2-2.20.1/src/windowMaker/ bedtools2-2.20.1/src/windowMaker/Makefile bedtools2-2.20.1/src/windowMaker/windowMaker.cpp bedtools2-2.20.1/src/windowMaker/windowMaker.h bedtools2-2.20.1/src/windowMaker/windowMakerMain.cpp bedtools2-2.20.1/src/windowBed/Makefile bedtools2-2.20.1/src/windowBed/windowBed.cpp bedtools2-2.20.1/src/windowBed/windowBed.h bedtools2-2.20.1/src/windowBed/windowMain.cpp bedtools2-2.20.1/src/utils/BamTools/ bedtools2-2.20.1/src/utils/BamTools-Ancillary/ bedtools2-2.20.1/src/utils/bedFile/ bedtools2-2.20.1/src/utils/bedFilePE/ bedtools2-2.20.1/src/utils/bedGraphFile/ bedtools2-2.20.1/src/utils/BinTree/ bedtools2-2.20.1/src/utils/BlockedIntervals/ bedtools2-2.20.1/src/utils/chromsweep/ bedtools2-2.20.1/src/utils/Contexts/ bedtools2-2.20.1/src/utils/Fasta/ bedtools2-2.20.1/src/utils/FileRecordTools/ bedtools2-2.20.1/src/utils/fileType/ bedtools2-2.20.1/src/utils/general/ bedtools2-2.20.1/src/utils/GenomeFile/ bedtools2-2.20.1/src/utils/gzstream/ bedtools2-2.20.1/src/utils/KeyListOps/ bedtools2-2.20.1/src/utils/lineFileUtilities/ bedtools2-2.20.1/src/utils/NewChromsweep/ bedtools2-2.20.1/src/utils/Point/ bedtools2-2.20.1/src/utils/RecordOutputMgr/ bedtools2-2.20.1/src/utils/sequenceUtilities/ bedtools2-2.20.1/src/utils/stringUtilities/ bedtools2-2.20.1/src/utils/tabFile/ bedtools2-2.20.1/src/utils/VectorOps/ bedtools2-2.20.1/src/utils/version/ bedtools2-2.20.1/src/utils/version/Makefile bedtools2-2.20.1/src/utils/version/version.cpp bedtools2-2.20.1/src/utils/version/version.h bedtools2-2.20.1/src/utils/version/version_git.h bedtools2-2.20.1/src/utils/version/version_release.txt bedtools2-2.20.1/src/utils/VectorOps/Makefile bedtools2-2.20.1/src/utils/VectorOps/VectorOps.cpp bedtools2-2.20.1/src/utils/VectorOps/VectorOps.h bedtools2-2.20.1/src/utils/tabFile/Makefile bedtools2-2.20.1/src/utils/tabFile/tabFile.cpp bedtools2-2.20.1/src/utils/tabFile/tabFile.h bedtools2-2.20.1/src/utils/stringUtilities/stringUtilities.h bedtools2-2.20.1/src/utils/sequenceUtilities/Makefile bedtools2-2.20.1/src/utils/sequenceUtilities/sequenceUtils.cpp bedtools2-2.20.1/src/utils/sequenceUtilities/sequenceUtils.h bedtools2-2.20.1/src/utils/RecordOutputMgr/Makefile bedtools2-2.20.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp bedtools2-2.20.1/src/utils/RecordOutputMgr/RecordOutputMgr.h bedtools2-2.20.1/src/utils/Point/Point.h bedtools2-2.20.1/src/utils/NewChromsweep/Makefile bedtools2-2.20.1/src/utils/NewChromsweep/NewChromsweep.cpp bedtools2-2.20.1/src/utils/NewChromsweep/NewChromsweep.h bedtools2-2.20.1/src/utils/lineFileUtilities/lineFileUtilities.h bedtools2-2.20.1/src/utils/KeyListOps/KeyListOps.cpp bedtools2-2.20.1/src/utils/KeyListOps/KeyListOps.h bedtools2-2.20.1/src/utils/KeyListOps/KeyListOpsMethods.cpp bedtools2-2.20.1/src/utils/KeyListOps/KeyListOpsMethods.h bedtools2-2.20.1/src/utils/KeyListOps/Makefile bedtools2-2.20.1/src/utils/gzstream/COPYING.LIB bedtools2-2.20.1/src/utils/gzstream/gzstream.C bedtools2-2.20.1/src/utils/gzstream/gzstream.h bedtools2-2.20.1/src/utils/gzstream/Makefile bedtools2-2.20.1/src/utils/gzstream/README bedtools2-2.20.1/src/utils/gzstream/version bedtools2-2.20.1/src/utils/GenomeFile/GenomeFile.cpp bedtools2-2.20.1/src/utils/GenomeFile/GenomeFile.h bedtools2-2.20.1/src/utils/GenomeFile/Makefile bedtools2-2.20.1/src/utils/GenomeFile/NewGenomeFile.cpp bedtools2-2.20.1/src/utils/GenomeFile/NewGenomeFile.h bedtools2-2.20.1/src/utils/general/BedtoolsTypes.h bedtools2-2.20.1/src/utils/general/BTlist.h bedtools2-2.20.1/src/utils/general/CompressionTools.cpp bedtools2-2.20.1/src/utils/general/CompressionTools.h bedtools2-2.20.1/src/utils/general/ErrorMsg.h bedtools2-2.20.1/src/utils/general/FreeList.h bedtools2-2.20.1/src/utils/general/InflateStreamBuf.h bedtools2-2.20.1/src/utils/general/Makefile bedtools2-2.20.1/src/utils/general/ParseTools.cpp bedtools2-2.20.1/src/utils/general/ParseTools.h bedtools2-2.20.1/src/utils/general/PushBackStreamBuf.cpp bedtools2-2.20.1/src/utils/general/PushBackStreamBuf.h bedtools2-2.20.1/src/utils/general/QuickString.cpp bedtools2-2.20.1/src/utils/general/QuickString.h bedtools2-2.20.1/src/utils/general/Tokenizer.cpp bedtools2-2.20.1/src/utils/general/Tokenizer.h bedtools2-2.20.1/src/utils/fileType/FileRecordTypeChecker.cpp bedtools2-2.20.1/src/utils/fileType/FileRecordTypeChecker.h bedtools2-2.20.1/src/utils/fileType/fileType.cpp bedtools2-2.20.1/src/utils/fileType/fileType.h bedtools2-2.20.1/src/utils/fileType/Makefile bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/ bedtools2-2.20.1/src/utils/FileRecordTools/FileRecordMergeMgr.cpp bedtools2-2.20.1/src/utils/FileRecordTools/FileRecordMergeMgr.h bedtools2-2.20.1/src/utils/FileRecordTools/FileRecordMgr.cpp bedtools2-2.20.1/src/utils/FileRecordTools/FileRecordMgr.h bedtools2-2.20.1/src/utils/FileRecordTools/Makefile bedtools2-2.20.1/src/utils/FileRecordTools/Records/ bedtools2-2.20.1/src/utils/FileRecordTools/Records/BamRecord.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/BamRecord.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed12Interval.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed3Interval.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed3Interval.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed4Interval.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed4Interval.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed5Interval.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed5Interval.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed6Interval.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/Bed6Interval.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/BedGraphInterval.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/BedGraphInterval.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/BedPlusInterval.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/BedPlusInterval.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/BlockMgr.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/BlockMgr.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/EmptyRecord.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/EmptyRecord.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/GffRecord.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/GffRecord.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/Makefile bedtools2-2.20.1/src/utils/FileRecordTools/Records/Record.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/Record.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/RecordKeyList.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/RecordKeyList.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/RecordMgr.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/RecordMgr.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/StrandQueue.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/StrandQueue.h bedtools2-2.20.1/src/utils/FileRecordTools/Records/VcfRecord.cpp bedtools2-2.20.1/src/utils/FileRecordTools/Records/VcfRecord.h bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/FileReader.cpp bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/FileReader.h bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/Makefile bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp bedtools2-2.20.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h bedtools2-2.20.1/src/utils/Fasta/Fasta.cpp bedtools2-2.20.1/src/utils/Fasta/Fasta.h bedtools2-2.20.1/src/utils/Fasta/LargeFileSupport.h bedtools2-2.20.1/src/utils/Fasta/Makefile bedtools2-2.20.1/src/utils/Fasta/split.cpp bedtools2-2.20.1/src/utils/Fasta/split.h bedtools2-2.20.1/src/utils/Contexts/ContextBase.cpp bedtools2-2.20.1/src/utils/Contexts/ContextBase.h bedtools2-2.20.1/src/utils/Contexts/ContextIntersect.cpp bedtools2-2.20.1/src/utils/Contexts/ContextIntersect.h bedtools2-2.20.1/src/utils/Contexts/ContextJaccard.cpp bedtools2-2.20.1/src/utils/Contexts/ContextJaccard.h bedtools2-2.20.1/src/utils/Contexts/ContextMap.cpp bedtools2-2.20.1/src/utils/Contexts/ContextMap.h bedtools2-2.20.1/src/utils/Contexts/ContextMerge.cpp bedtools2-2.20.1/src/utils/Contexts/ContextMerge.h bedtools2-2.20.1/src/utils/Contexts/ContextSample.cpp bedtools2-2.20.1/src/utils/Contexts/ContextSample.h bedtools2-2.20.1/src/utils/Contexts/Makefile bedtools2-2.20.1/src/utils/chromsweep/chromsweep.cpp bedtools2-2.20.1/src/utils/chromsweep/chromsweep.h bedtools2-2.20.1/src/utils/chromsweep/Makefile bedtools2-2.20.1/src/utils/BlockedIntervals/BlockedIntervals.cpp bedtools2-2.20.1/src/utils/BlockedIntervals/BlockedIntervals.h bedtools2-2.20.1/src/utils/BlockedIntervals/Makefile bedtools2-2.20.1/src/utils/BinTree/BinTree.cpp bedtools2-2.20.1/src/utils/BinTree/BinTree.h bedtools2-2.20.1/src/utils/BinTree/Makefile bedtools2-2.20.1/src/utils/bedGraphFile/bedGraphFile.cpp bedtools2-2.20.1/src/utils/bedGraphFile/bedGraphFile.h bedtools2-2.20.1/src/utils/bedGraphFile/Makefile bedtools2-2.20.1/src/utils/bedFilePE/bedFilePE.cpp bedtools2-2.20.1/src/utils/bedFilePE/bedFilePE.h bedtools2-2.20.1/src/utils/bedFilePE/Makefile bedtools2-2.20.1/src/utils/bedFile/bedFile.cpp bedtools2-2.20.1/src/utils/bedFile/bedFile.h bedtools2-2.20.1/src/utils/bedFile/Makefile bedtools2-2.20.1/src/utils/BamTools-Ancillary/BamAncillary.cpp bedtools2-2.20.1/src/utils/BamTools-Ancillary/BamAncillary.h bedtools2-2.20.1/src/utils/BamTools-Ancillary/Makefile bedtools2-2.20.1/src/utils/BamTools/.gitignore bedtools2-2.20.1/src/utils/BamTools/LICENSE bedtools2-2.20.1/src/utils/BamTools/Makefile bedtools2-2.20.1/src/utils/BamTools/src/ bedtools2-2.20.1/src/utils/BamTools/src/api/ bedtools2-2.20.1/src/utils/BamTools/src/shared/ bedtools2-2.20.1/src/utils/BamTools/src/shared/bamtools_global.h bedtools2-2.20.1/src/utils/BamTools/src/api/algorithms/ bedtools2-2.20.1/src/utils/BamTools/src/api/api_global.h bedtools2-2.20.1/src/utils/BamTools/src/api/BamAlgorithms.h bedtools2-2.20.1/src/utils/BamTools/src/api/BamAlignment.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/BamAlignment.h bedtools2-2.20.1/src/utils/BamTools/src/api/BamAux.h bedtools2-2.20.1/src/utils/BamTools/src/api/BamConstants.h bedtools2-2.20.1/src/utils/BamTools/src/api/BamIndex.h bedtools2-2.20.1/src/utils/BamTools/src/api/BamMultiReader.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/BamMultiReader.h bedtools2-2.20.1/src/utils/BamTools/src/api/BamReader.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/BamReader.h bedtools2-2.20.1/src/utils/BamTools/src/api/BamWriter.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/BamWriter.h bedtools2-2.20.1/src/utils/BamTools/src/api/IBamIODevice.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/ bedtools2-2.20.1/src/utils/BamTools/src/api/SamConstants.h bedtools2-2.20.1/src/utils/BamTools/src/api/SamHeader.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/SamHeader.h bedtools2-2.20.1/src/utils/BamTools/src/api/SamProgram.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/SamProgram.h bedtools2-2.20.1/src/utils/BamTools/src/api/SamProgramChain.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/SamProgramChain.h bedtools2-2.20.1/src/utils/BamTools/src/api/SamReadGroup.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/SamReadGroup.h bedtools2-2.20.1/src/utils/BamTools/src/api/SamReadGroupDictionary.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/SamReadGroupDictionary.h bedtools2-2.20.1/src/utils/BamTools/src/api/SamSequence.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/SamSequence.h bedtools2-2.20.1/src/utils/BamTools/src/api/SamSequenceDictionary.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/SamSequenceDictionary.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/ bedtools2-2.20.1/src/utils/BamTools/src/api/internal/index/ bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/ bedtools2-2.20.1/src/utils/BamTools/src/api/internal/sam/ bedtools2-2.20.1/src/utils/BamTools/src/api/internal/utils/ bedtools2-2.20.1/src/utils/BamTools/src/api/internal/utils/BamException_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/utils/BamException_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/sam/SamFormatParser_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/sam/SamFormatParser_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/sam/SamFormatPrinter_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/sam/SamFormatPrinter_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/sam/SamHeaderValidator_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/sam/SamHeaderValidator_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/sam/SamHeaderVersion_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamFile_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamFile_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamFtp_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamFtp_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamHttp_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamHttp_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamPipe_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BamPipe_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/ByteArray_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/ByteArray_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/HostAddress_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/HostAddress_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/HostInfo_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/HostInfo_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/HttpHeader_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/HttpHeader_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/ILocalIODevice_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/ILocalIODevice_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/NetUnix_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/NetWin_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/RollingBuffer_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/RollingBuffer_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/StdStreamDevice_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/TcpSocket_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/TcpSocket_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_unix_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_win_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/index/BamIndexFactory_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/index/BamIndexFactory_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/index/BamStandardIndex_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/index/BamStandardIndex_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/index/BamToolsIndex_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/index/BamToolsIndex_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamHeader_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamHeader_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamMultiReader_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamMultiReader_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamRandomAccessController_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamRandomAccessController_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamReader_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamWriter_p.cpp bedtools2-2.20.1/src/utils/BamTools/src/api/internal/bam/BamWriter_p.h bedtools2-2.20.1/src/utils/BamTools/src/api/algorithms/Sort.h bedtools2-2.20.1/src/unionBedGraphs/Makefile bedtools2-2.20.1/src/unionBedGraphs/unionBedGraphs.cpp bedtools2-2.20.1/src/unionBedGraphs/unionBedGraphs.h bedtools2-2.20.1/src/unionBedGraphs/unionBedGraphsMain.cpp bedtools2-2.20.1/src/tagBam/Makefile bedtools2-2.20.1/src/tagBam/tagBam.cpp bedtools2-2.20.1/src/tagBam/tagBam.h bedtools2-2.20.1/src/tagBam/tagBamMain.cpp bedtools2-2.20.1/src/subtractBed/Makefile bedtools2-2.20.1/src/subtractBed/subtractBed.cpp bedtools2-2.20.1/src/subtractBed/subtractBed.h bedtools2-2.20.1/src/subtractBed/subtractMain.cpp bedtools2-2.20.1/src/sortBed/Makefile bedtools2-2.20.1/src/sortBed/sortBed.cpp bedtools2-2.20.1/src/sortBed/sortBed.h bedtools2-2.20.1/src/sortBed/sortMain.cpp bedtools2-2.20.1/src/slopBed/Makefile bedtools2-2.20.1/src/slopBed/slopBed.cpp bedtools2-2.20.1/src/slopBed/slopBed.h bedtools2-2.20.1/src/slopBed/slopBedMain.cpp bedtools2-2.20.1/src/shuffleBed/Makefile bedtools2-2.20.1/src/shuffleBed/shuffleBed.cpp bedtools2-2.20.1/src/shuffleBed/shuffleBed.h bedtools2-2.20.1/src/shuffleBed/shuffleBedMain.cpp bedtools2-2.20.1/src/sampleFile/Makefile bedtools2-2.20.1/src/sampleFile/SampleFile.cpp bedtools2-2.20.1/src/sampleFile/SampleFile.h bedtools2-2.20.1/src/sampleFile/sampleMain.cpp bedtools2-2.20.1/src/reldist/Makefile bedtools2-2.20.1/src/reldist/reldist.cpp bedtools2-2.20.1/src/reldist/reldist.h bedtools2-2.20.1/src/reldist/reldistMain.cpp bedtools2-2.20.1/src/regressTest/Makefile bedtools2-2.20.1/src/regressTest/RegressTest.cpp bedtools2-2.20.1/src/regressTest/RegressTest.h bedtools2-2.20.1/src/regressTest/regressTestMain.cpp bedtools2-2.20.1/src/randomBed/Makefile bedtools2-2.20.1/src/randomBed/randomBed.cpp bedtools2-2.20.1/src/randomBed/randomBed.h bedtools2-2.20.1/src/randomBed/randomBedMain.cpp bedtools2-2.20.1/src/pairToPair/Makefile bedtools2-2.20.1/src/pairToPair/pairToPair.cpp bedtools2-2.20.1/src/pairToPair/pairToPair.h bedtools2-2.20.1/src/pairToPair/pairToPairMain.cpp bedtools2-2.20.1/src/pairToBed/Makefile bedtools2-2.20.1/src/pairToBed/pairToBed.cpp bedtools2-2.20.1/src/pairToBed/pairToBed.h bedtools2-2.20.1/src/pairToBed/pairToBedMain.cpp bedtools2-2.20.1/src/nucBed/LargeFileSupport.h bedtools2-2.20.1/src/nucBed/Makefile bedtools2-2.20.1/src/nucBed/nucBed.cpp bedtools2-2.20.1/src/nucBed/nucBed.h bedtools2-2.20.1/src/nucBed/nucBedMain.cpp bedtools2-2.20.1/src/nekSandbox1/FormatGuess.h bedtools2-2.20.1/src/nekSandbox1/Makefile bedtools2-2.20.1/src/nekSandbox1/nekSandboxMain.cpp bedtools2-2.20.1/src/multiIntersectBed/Makefile bedtools2-2.20.1/src/multiIntersectBed/multiIntersectBed.cpp bedtools2-2.20.1/src/multiIntersectBed/multiIntersectBed.h bedtools2-2.20.1/src/multiIntersectBed/multiIntersectBedMain.cpp bedtools2-2.20.1/src/multiBamCov/Makefile bedtools2-2.20.1/src/multiBamCov/multiBamCov.cpp bedtools2-2.20.1/src/multiBamCov/multiBamCov.h bedtools2-2.20.1/src/multiBamCov/multiBamCovMain.cpp bedtools2-2.20.1/src/mergeFile/Makefile bedtools2-2.20.1/src/mergeFile/mergeFile.cpp bedtools2-2.20.1/src/mergeFile/mergeFile.h bedtools2-2.20.1/src/mergeFile/mergeMain.cpp bedtools2-2.20.1/src/maskFastaFromBed/Makefile bedtools2-2.20.1/src/maskFastaFromBed/maskFastaFromBed.cpp bedtools2-2.20.1/src/maskFastaFromBed/maskFastaFromBed.h bedtools2-2.20.1/src/maskFastaFromBed/maskFastaFromBedMain.cpp bedtools2-2.20.1/src/mapFile/Makefile bedtools2-2.20.1/src/mapFile/mapFile.cpp bedtools2-2.20.1/src/mapFile/mapFile.h bedtools2-2.20.1/src/mapFile/mapMain.cpp bedtools2-2.20.1/src/linksBed/linksBed.cpp bedtools2-2.20.1/src/linksBed/linksBed.h bedtools2-2.20.1/src/linksBed/linksMain.cpp bedtools2-2.20.1/src/linksBed/Makefile bedtools2-2.20.1/src/jaccard/Jaccard.cpp bedtools2-2.20.1/src/jaccard/Jaccard.h bedtools2-2.20.1/src/jaccard/jaccardMain.cpp bedtools2-2.20.1/src/jaccard/Makefile bedtools2-2.20.1/src/intersectFile/intersectFile.cpp bedtools2-2.20.1/src/intersectFile/intersectFile.h bedtools2-2.20.1/src/intersectFile/intersectMain.cpp bedtools2-2.20.1/src/intersectFile/Makefile bedtools2-2.20.1/src/groupBy/groupBy.cpp bedtools2-2.20.1/src/groupBy/Makefile bedtools2-2.20.1/src/getOverlap/getOverlap.cpp bedtools2-2.20.1/src/getOverlap/Makefile bedtools2-2.20.1/src/genomeCoverageBed/genomeCoverageBed.cpp bedtools2-2.20.1/src/genomeCoverageBed/genomeCoverageBed.h bedtools2-2.20.1/src/genomeCoverageBed/genomeCoverageMain.cpp bedtools2-2.20.1/src/genomeCoverageBed/Makefile bedtools2-2.20.1/src/flankBed/flankBed.cpp bedtools2-2.20.1/src/flankBed/flankBed.h bedtools2-2.20.1/src/flankBed/flankBedMain.cpp bedtools2-2.20.1/src/flankBed/Makefile bedtools2-2.20.1/src/fastaFromBed/fastaFromBed.cpp bedtools2-2.20.1/src/fastaFromBed/fastaFromBed.h bedtools2-2.20.1/src/fastaFromBed/fastaFromBedMain.cpp bedtools2-2.20.1/src/fastaFromBed/Makefile bedtools2-2.20.1/src/expand/expand.cpp bedtools2-2.20.1/src/expand/Makefile bedtools2-2.20.1/src/coverageBed/coverageBed.cpp bedtools2-2.20.1/src/coverageBed/coverageBed.h bedtools2-2.20.1/src/coverageBed/coverageMain.cpp bedtools2-2.20.1/src/coverageBed/Makefile bedtools2-2.20.1/src/complementBed/complementBed.cpp bedtools2-2.20.1/src/complementBed/complementBed.h bedtools2-2.20.1/src/complementBed/complementMain.cpp bedtools2-2.20.1/src/complementBed/Makefile bedtools2-2.20.1/src/clusterBed/clusterBed.cpp bedtools2-2.20.1/src/clusterBed/clusterBed.h bedtools2-2.20.1/src/clusterBed/clusterMain.cpp bedtools2-2.20.1/src/clusterBed/Makefile bedtools2-2.20.1/src/closestBed/closestBed.cpp bedtools2-2.20.1/src/closestBed/closestBed.h bedtools2-2.20.1/src/closestBed/closestMain.cpp bedtools2-2.20.1/src/closestBed/Makefile bedtools2-2.20.1/src/bedToIgv/bedToIgv.cpp bedtools2-2.20.1/src/bedToIgv/Makefile bedtools2-2.20.1/src/bedToBam/bedToBam.cpp bedtools2-2.20.1/src/bedToBam/Makefile bedtools2-2.20.1/src/bedpeToBam/bedpeToBam.cpp bedtools2-2.20.1/src/bedpeToBam/Makefile bedtools2-2.20.1/src/bedpeToBam/notes.txt bedtools2-2.20.1/src/bed12ToBed6/bed12ToBed6.cpp bedtools2-2.20.1/src/bed12ToBed6/Makefile bedtools2-2.20.1/src/bamToFastq/bamToFastq.cpp bedtools2-2.20.1/src/bamToFastq/bamToFastq.h bedtools2-2.20.1/src/bamToFastq/bamToFastqMain.cpp bedtools2-2.20.1/src/bamToFastq/Makefile bedtools2-2.20.1/src/bamToBed/bamToBed.cpp bedtools2-2.20.1/src/bamToBed/Makefile bedtools2-2.20.1/src/annotateBed/annotateBed.cpp bedtools2-2.20.1/src/annotateBed/annotateBed.h bedtools2-2.20.1/src/annotateBed/annotateMain.cpp bedtools2-2.20.1/src/annotateBed/Makefile bedtools2-2.20.1/scripts/makeBashScripts.py bedtools2-2.20.1/genomes/human.hg18.genome bedtools2-2.20.1/genomes/human.hg19.genome bedtools2-2.20.1/genomes/mouse.mm10.genome.txt bedtools2-2.20.1/genomes/mouse.mm8.genome bedtools2-2.20.1/genomes/mouse.mm9.genome bedtools2-2.20.1/docs/_static/ bedtools2-2.20.1/docs/bedtools.ai bedtools2-2.20.1/docs/bedtools.png bedtools2-2.20.1/docs/build.sh bedtools2-2.20.1/docs/conf.py bedtools2-2.20.1/docs/content/ bedtools2-2.20.1/docs/index.rst bedtools2-2.20.1/docs/make.bat bedtools2-2.20.1/docs/Makefile bedtools2-2.20.1/docs/templates/ bedtools2-2.20.1/docs/themes/ bedtools2-2.20.1/docs/themes/rtd/ bedtools2-2.20.1/docs/themes/rtd/static/ bedtools2-2.20.1/docs/themes/rtd/theme.conf bedtools2-2.20.1/docs/themes/rtd/static/rtd.css_t bedtools2-2.20.1/docs/templates/page.html bedtools2-2.20.1/docs/templates/sidebar-intro.html bedtools2-2.20.1/docs/content/advanced-usage.rst bedtools2-2.20.1/docs/content/bedtools-suite.rst bedtools2-2.20.1/docs/content/example-usage.rst bedtools2-2.20.1/docs/content/faq.rst bedtools2-2.20.1/docs/content/general-usage.rst bedtools2-2.20.1/docs/content/history.rst bedtools2-2.20.1/docs/content/images/ bedtools2-2.20.1/docs/content/installation.rst bedtools2-2.20.1/docs/content/overview.rst bedtools2-2.20.1/docs/content/quick-start.rst bedtools2-2.20.1/docs/content/related-tools.rst bedtools2-2.20.1/docs/content/tips-and-tricks.rst bedtools2-2.20.1/docs/content/tools/ bedtools2-2.20.1/docs/content/tools/annotate.rst bedtools2-2.20.1/docs/content/tools/bamtobed.rst bedtools2-2.20.1/docs/content/tools/bamtofastq.rst bedtools2-2.20.1/docs/content/tools/bed12tobed6.rst bedtools2-2.20.1/docs/content/tools/bedpetobam.rst bedtools2-2.20.1/docs/content/tools/bedtobam.rst bedtools2-2.20.1/docs/content/tools/closest.rst bedtools2-2.20.1/docs/content/tools/cluster.rst bedtools2-2.20.1/docs/content/tools/complement.rst bedtools2-2.20.1/docs/content/tools/coverage.rst bedtools2-2.20.1/docs/content/tools/expand.rst bedtools2-2.20.1/docs/content/tools/flank.rst bedtools2-2.20.1/docs/content/tools/genomecov.rst bedtools2-2.20.1/docs/content/tools/getfasta.rst bedtools2-2.20.1/docs/content/tools/groupby.rst bedtools2-2.20.1/docs/content/tools/igv.rst bedtools2-2.20.1/docs/content/tools/intersect.rst bedtools2-2.20.1/docs/content/tools/jaccard.rst bedtools2-2.20.1/docs/content/tools/links.rst bedtools2-2.20.1/docs/content/tools/makewindows.rst bedtools2-2.20.1/docs/content/tools/map.rst bedtools2-2.20.1/docs/content/tools/maskfasta.rst bedtools2-2.20.1/docs/content/tools/merge.rst bedtools2-2.20.1/docs/content/tools/multicov.rst bedtools2-2.20.1/docs/content/tools/multiinter.rst bedtools2-2.20.1/docs/content/tools/nuc.rst bedtools2-2.20.1/docs/content/tools/overlap.rst bedtools2-2.20.1/docs/content/tools/pairtobed.rst bedtools2-2.20.1/docs/content/tools/pairtopair.rst bedtools2-2.20.1/docs/content/tools/random.rst bedtools2-2.20.1/docs/content/tools/reldist.rst bedtools2-2.20.1/docs/content/tools/shuffle.rst bedtools2-2.20.1/docs/content/tools/slop.rst bedtools2-2.20.1/docs/content/tools/sort.rst bedtools2-2.20.1/docs/content/tools/subtract.rst bedtools2-2.20.1/docs/content/tools/tag.rst bedtools2-2.20.1/docs/content/tools/unionbedg.rst bedtools2-2.20.1/docs/content/tools/window.rst bedtools2-2.20.1/docs/content/images/bedtoolsMenu.png bedtools2-2.20.1/docs/content/images/galaxy-bedtools.png bedtools2-2.20.1/docs/content/images/github-zip-button.png bedtools2-2.20.1/docs/content/images/memory-comparo.png bedtools2-2.20.1/docs/content/images/speed-comparo.png bedtools2-2.20.1/docs/content/images/tool-glyphs/ bedtools2-2.20.1/docs/content/images/tool-glyphs/cluster-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/complement-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/flank-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/genomecov-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/getfasta-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/intersect-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/jaccard-glyph.ai bedtools2-2.20.1/docs/content/images/tool-glyphs/jaccard-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/map-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/map-glyph.svg bedtools2-2.20.1/docs/content/images/tool-glyphs/map-speed-comparo.png bedtools2-2.20.1/docs/content/images/tool-glyphs/maskfasta-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/maskfasta-glyph.svg bedtools2-2.20.1/docs/content/images/tool-glyphs/merge-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/reldist-glyph.ai bedtools2-2.20.1/docs/content/images/tool-glyphs/reldist-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/reldist-plot.png bedtools2-2.20.1/docs/content/images/tool-glyphs/shuffle-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/slop-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/subtract-glyph.png bedtools2-2.20.1/docs/content/images/tool-glyphs/window-glyph.png bedtools2-2.20.1/docs/_static/labibi.css bedtools2-2.20.1/docs/_static/labibi.js bedtools2-2.20.1/data/aluY.chr1.bed.gz bedtools2-2.20.1/data/gerp.chr1.bed.gz bedtools2-2.20.1/data/knownGene.hg18.chr21.bed bedtools2-2.20.1/data/knownGene.hg18.chr21.short.bed bedtools2-2.20.1/data/refseq.chr1.exons.bed.gz bedtools2-2.20.1/data/simpleRepeats.chr1.bed.gz sudo -u fink-bld [ENV] sh -c /tmp/fink.800yR make -w make: Entering directory `/sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1' Building BEDTools: ========================================================= DETECTED_VERSION = v2.20.1 CURRENT_VERSION = v2.20.1 * Creating BamTools API - Building in src/utils/bedFile - Building in src/utils/BinTree - Building in src/utils/version - Building in src/utils/bedGraphFile - Building in src/utils/Contexts - Building in src/utils/general - Building in src/utils/chromsweep - Building in src/utils/FileRecordTools * compiling version.cpp * compiling BinTree.cpp * compiling bedGraphFile.cpp * compiling chromsweep.cpp * compiling ContextBase.cpp - Building in FileReaders * compiling QuickString.cpp * compiling bedFile.cpp * compiling FileReader.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' clangclang: warning: argument unused during compilation: '-L/sw/lib' : warning: argument unused during compilation: '-L/sw/lib' In file included from BinTree.cpp:1: ./BinTree.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from QuickString.cpp:1: ./QuickString.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' * compiling ContextIntersect.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from ContextBase.cpp:8: In file included from ./ContextBase.h:22: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ In file included from ContextIntersect.cpp:8: In file included from ./ContextIntersect.h:11: In file included from ./ContextBase.h:22: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ In file included from FileReader.cpp:3: In file included from ./FileReader.h:12: In file included from ./BufferedStreamMgr.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 1 warning generated. * compiling ParseTools.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from ParseTools.cpp:1: ./ParseTools.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 1 warning generated. * compiling SingleLineDelimTransferBuffer.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from SingleLineDelimTransferBuffer.cpp:1: ./SingleLineDelimTransferBuffer.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ - Building in Records * compiling RecordMgr.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from RecordMgr.cpp:1: In file included from ./RecordMgr.h:12: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from RecordMgr.cpp:1: In file included from ./RecordMgr.h:12: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from BinTree.cpp:1: In file included from ./BinTree.h:19: In file included from ../../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../../utils//FileRecordTools/Records/Record.h:15: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ BinTree.cpp:182:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (binNum < 0 || binNum >= NUM_BINS) { ~~~~~~ ^ ~ 1 warning generated. * compiling PushBackStreamBuf.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 1 warning generated. - Building in src/utils/gzstream g++ -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -c -o ../../../obj//gzstream.o gzstream.C -I. 1 warning generated. 1 warning generated. * compiling SingleLineDelimTextFileReader.cpp * compiling ContextMap.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from SingleLineDelimTextFileReader.cpp:1: ./SingleLineDelimTextFileReader.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from SingleLineDelimTextFileReader.cpp:1: In file included from ./SingleLineDelimTextFileReader.h:13: ./FileReader.h:4:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' * compiling CompressionTools.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from CompressionTools.cpp:8: ./CompressionTools.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from CompressionTools.cpp:8: In file included from ./CompressionTools.h:14: In file included from ./BTlist.h:28: ./FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 3 warnings generated. * compiling BamFileReader.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from BamFileReader.cpp:1: ./BamFileReader.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from BamFileReader.cpp:1: In file included from ./BamFileReader.h:13: ./FileReader.h:4:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from RecordMgr.cpp:1: In file included from ./RecordMgr.h:12: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling ContextSample.cpp * compiling Record.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Record.cpp:2: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from Record.cpp:2: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 2 warnings generated. In file included from ContextMap.cpp:8: In file included from ./ContextMap.h:11: In file included from ./ContextIntersect.h:11: In file included from ./ContextBase.h:22: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling Tokenizer.cpp In file included from SingleLineDelimTextFileReader.cpp:1: In file included from ./SingleLineDelimTextFileReader.h:13: In file included from ./FileReader.h:12: In file included from ./BufferedStreamMgr.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Tokenizer.cpp:7: ./Tokenizer.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from Tokenizer.cpp:7: In file included from ./Tokenizer.h:13: ./QuickString.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from BamFileReader.cpp:1: In file included from ./BamFileReader.h:13: In file included from ./FileReader.h:12: In file included from ./BufferedStreamMgr.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 3 warnings generated. - Building in src/utils/fileType * compiling fileType.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 3 warnings generated. * compiling BufferedStreamMgr.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from BufferedStreamMgr.cpp:8: ./BufferedStreamMgr.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 1 warning generated. * compiling EmptyRecord.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from EmptyRecord.cpp:9: In file included from ./EmptyRecord.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from EmptyRecord.cpp:9: In file included from ./EmptyRecord.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from ContextSample.cpp:7: In file included from ./ContextSample.h:11: In file included from ./ContextBase.h:22: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ In file included from Record.cpp:2: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ - Building in src/utils/bedFilePE 2 warnings generated. * compiling bedFilePE.cpp - Building in src/utils/KeyListOps * compiling KeyListOps.cpp 3 warnings generated. * compiling FileRecordTypeChecker.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' In file included from KeyListOps.cpp:7: In file included from ./KeyListOps.h:11: ./KeyListOpsMethods.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' In file included from FileRecordTypeChecker.cpp:2: ./FileRecordTypeChecker.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 1 warning generated. * compiling ContextMerge.cpp In file included from BufferedStreamMgr.cpp:8: In file included from ./BufferedStreamMgr.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ clang: warning: argument unused during compilation: '-L/sw/lib' In file included from EmptyRecord.cpp:9: In file included from ./EmptyRecord.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 2 warnings generated. * compiling InputStreamMgr.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from InputStreamMgr.cpp:8: ./InputStreamMgr.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from InputStreamMgr.cpp:8: In file included from ./InputStreamMgr.h:13: ../../../utils//general/PushBackStreamBuf.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 3 warnings generated. - Building in src/utils/NewChromsweep * compiling NewChromsweep.cpp In file included from KeyListOps.cpp:7: In file included from ./KeyListOps.h:11: In file included from ./KeyListOpsMethods.h:17: In file included from ../../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../../utils//FileRecordTools/Records/Record.h:15: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ clang: warning: argument unused during compilation: '-L/sw/lib' In file included from NewChromsweep.cpp:13: ./NewChromsweep.h:15:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ ./FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling KeyListOpsMethods.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from KeyListOpsMethods.cpp:8: ./KeyListOpsMethods.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from ContextMerge.cpp:9: In file included from ./ContextMerge.h:11: In file included from ./ContextBase.h:22: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ bedFilePE.cpp:287:31: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { ~~~~~~~~~~ ^ ~ bedFilePE.cpp:287:49: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { ~~~~~~~~ ^ ~ bedFilePE.cpp:287:69: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { ~~~~~~~~~~ ^ ~ bedFilePE.cpp:287:87: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { ~~~~~~~~ ^ ~ bedFilePE.cpp:381:31: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { ~~~~~~~~~~ ^ ~ bedFilePE.cpp:381:49: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { ~~~~~~~~ ^ ~ bedFilePE.cpp:381:69: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { ~~~~~~~~~~ ^ ~ bedFilePE.cpp:381:87: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) { ~~~~~~~~ ^ ~ 3 warnings generated. * compiling Bed3Interval.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Bed3Interval.cpp:2: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from Bed3Interval.cpp:2: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 2 warnings generated. * compiling ContextJaccard.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from NewChromsweep.cpp:13: In file included from ./NewChromsweep.h:19: In file included from ../../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../../utils//FileRecordTools/Records/Record.h:15: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 2 warnings generated. - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 1 warning generated. * compiling Bed4Interval.cpp 2 warnings generated. clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/utils/tabFile In file included from Bed4Interval.cpp:1: In file included from ./Bed4Interval.h:13: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from Bed4Interval.cpp:1: In file included from ./Bed4Interval.h:13: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ * compiling tabFile.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from KeyListOpsMethods.cpp:8: In file included from ./KeyListOpsMethods.h:17: In file included from ../../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../../utils//FileRecordTools/Records/Record.h:15: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 2 warnings generated. * compiling BedGraphInterval.cpp - Building in src/utils/BamTools * compiling BamAlignment.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from BedGraphInterval.cpp:1: In file included from ./BedGraphInterval.h:12: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from BedGraphInterval.cpp:1: In file included from ./BedGraphInterval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Bed3Interval.cpp:2: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ In file included from ContextJaccard.cpp:8: In file included from ./ContextJaccard.h:11: In file included from ./ContextIntersect.h:11: In file included from ./ContextBase.h:22: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 8 warnings generated. * compiling Bed5Interval.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Bed5Interval.cpp:1: In file included from ./Bed5Interval.h:12: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from Bed5Interval.cpp:1: In file included from ./Bed5Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 3 warnings generated. - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-Lsrc/utils/BamTools//lib' In file included from Bed4Interval.cpp:1: In file included from ./Bed4Interval.h:13: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 1 warning generated. In file included from BedGraphInterval.cpp:1: In file included from ./BedGraphInterval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling BamMultiReader.cpp 3 warnings generated. clang: warning: argument unused during compilation: '-L/sw/lib' 2 warnings generated. * compiling BamAncillary.cpp - Building in src/utils/BlockedIntervals * compiling BlockedIntervals.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-Lsrc/utils/BamTools//lib' clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-Lsrc/utils/BamTools//lib' 3 warnings generated. * compiling Bed6Interval.cpp * compiling BamReader.cpp - Building in src/utils/Fasta * compiling Fasta.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Bed6Interval.cpp:1: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from Bed6Interval.cpp:1: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Bed5Interval.cpp:1: In file included from ./Bed5Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 3 warnings generated. * compiling BamWriter.cpp clang: warning: argument unused during compilation: '-L/sw/lib' Fasta.cpp:29:14: warning: implicit conversion of NULL constant to 'int' [-Wnull-conversion] length = NULL; ~ ^~~~ 0 Fasta.cpp:32:17: warning: implicit conversion of NULL constant to 'int' [-Wnull-conversion] line_blen = NULL; ~ ^~~~ 0 Fasta.cpp:33:17: warning: implicit conversion of NULL constant to 'int' [-Wnull-conversion] line_len = NULL; ~ ^~~~ 0 In file included from Bed6Interval.cpp:1: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling split.cpp * compiling SamHeader.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BedPlusInterval.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from BedPlusInterval.cpp:1: In file included from ./BedPlusInterval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from BedPlusInterval.cpp:1: In file included from ./BedPlusInterval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 3 warnings generated. - Building in src/utils/VectorOps * compiling VectorOps.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling Bed12Interval.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Bed12Interval.cpp:1: In file included from ./Bed12Interval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from Bed12Interval.cpp:1: In file included from ./Bed12Interval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ * compiling SamProgram.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BamRecord.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from BamRecord.cpp:8: In file included from ./BamRecord.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from BamRecord.cpp:8: In file included from ./BamRecord.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ - Building in src/utils/GenomeFile * compiling GenomeFile.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from BedPlusInterval.cpp:1: In file included from ./BedPlusInterval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling VcfRecord.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from VcfRecord.cpp:8: In file included from ./VcfRecord.h:11: In file included from ./BedPlusInterval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from VcfRecord.cpp:8: In file included from ./VcfRecord.h:11: In file included from ./BedPlusInterval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 3 warnings generated. * compiling SamProgramChain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Bed12Interval.cpp:1: In file included from ./Bed12Interval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 3 warnings generated. - Building in src/utils/RecordOutputMgr * compiling RecordOutputMgr.cpp In file included from BamRecord.cpp:8: In file included from ./BamRecord.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 3 warnings generated. * compiling SamReadGroup.cpp In file included from VcfRecord.cpp:8: In file included from ./VcfRecord.h:11: In file included from ./BedPlusInterval.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 3 warnings generated. - Building in src/annotateBed * compiling annotateMain.cpp 3 warnings generated. * compiling GffRecord.cpp - Building in src/bamToBed * compiling bamToBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' In file included from RecordOutputMgr.cpp:8: ./RecordOutputMgr.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' In file included from GffRecord.cpp:1: In file included from ./GffRecord.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from GffRecord.cpp:1: In file included from ./GffRecord.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' * compiling SamReadGroupDictionary.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling annotateBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/bamToFastq * compiling bamToFastqMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling NewGenomeFile.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from GffRecord.cpp:1: In file included from ./GffRecord.h:11: In file included from ./Bed6Interval.h:12: In file included from ./Bed3Interval.h:11: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ In file included from RecordOutputMgr.cpp:8: In file included from ./RecordOutputMgr.h:13: In file included from ../../utils//Contexts/ContextBase.h:22: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 3 warnings generated. * compiling RecordKeyList.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from RecordKeyList.cpp:1: ./RecordKeyList.h:14:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from RecordKeyList.cpp:1: In file included from ./RecordKeyList.h:16: ./Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from RecordKeyList.cpp:1: In file included from ./RecordKeyList.h:16: In file included from ./Record.h:13: ../../../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ * compiling SamSequence.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling bamToFastq.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 2 warnings generated. * compiling BlockMgr.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from BlockMgr.cpp:8: ./BlockMgr.h:14:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from BlockMgr.cpp:8: In file included from ./BlockMgr.h:16: ../../../utils//fileType/FileRecordTypeChecker.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ * compiling SamSequenceDictionary.cpp NewGenomeFile.cpp:86:11: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (i < 0 || i >= _chromList.size()) { ~ ^ ~ clang: warning: argument unused during compilation: '-L/sw/lib' In file included from RecordKeyList.cpp:1: In file included from ./RecordKeyList.h:16: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling StrandQueue.cpp 1 warning generated. clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BamHeader_p.cpp In file included from StrandQueue.cpp:8: ./StrandQueue.h:10:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' 4 warnings generated. * compiling BamMultiReader_p.cpp * compiling BamRandomAccessController_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/bedToBam * compiling bedToBam.cpp clang: warning: argument unused during compilation: '-L/sw/lib' ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 3 warnings generated. - Building in src/bedpeToBam * compiling bedpeToBam.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BamReader_p.cpp - Building in src/bedToIgv * compiling bedToIgv.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' In file included from StrandQueue.cpp:8: In file included from ./StrandQueue.h:16: In file included from ./Record.h:15: ../../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ - Building in src/bed12ToBed6 * compiling bed12ToBed6.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 2 warnings generated. * compiling FileRecordMgr.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from FileRecordMgr.cpp:2: ./FileRecordMgr.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ bedToBam.cpp:121:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (mapQual < 0 || mapQual > 255) { ~~~~~~~ ^ ~ * compiling BamWriter_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' bedpeToBam.cpp:119:17: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (mapQual < 0 || mapQual > 255) { ~~~~~~~ ^ ~ 1 warning generated. * compiling BamIndexFactory_p.cpp In file included from FileRecordMgr.cpp:2: In file included from ./FileRecordMgr.h:19: In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:15: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/closestBed * compiling closestMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/clusterBed * compiling clusterMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling closestBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/complementBed * compiling complementMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 2 warnings generated. * compiling FileRecordMergeMgr.cpp 1 warning generated. * compiling BamStandardIndex_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from FileRecordMergeMgr.cpp:9: In file included from ./FileRecordMergeMgr.h:11: ./FileRecordMgr.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ * compiling clusterBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BamToolsIndex_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from FileRecordMergeMgr.cpp:9: In file included from ./FileRecordMergeMgr.h:11: In file included from ./FileRecordMgr.h:19: In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:15: ../../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ - Building in src/coverageBed * compiling coverageMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BamDeviceFactory_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling complementBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 2 warnings generated. * compiling coverageBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BamFile_p.cpp * compiling BamFtp_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BamHttp_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/expand * compiling expand.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BamPipe_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/fastaFromBed * compiling fastaFromBedMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling BgzfStream_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling fastaFromBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling ByteArray_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling HostAddress_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling HostInfo_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/flankBed * compiling flankBedMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/genomeCoverageBed * compiling genomeCoverageMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling HttpHeader_p.cpp * compiling flankBed.cpp - Building in src/getOverlap * compiling getOverlap.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare] return m_ip4Address < m_ip4Address; ^ * compiling genomeCoverageBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 1 warning generated. - Building in src/groupBy * compiling groupBy.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling ILocalIODevice_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' src/api/internal/io/HttpHeader_p.cpp:33:19: warning: unused variable 'TAB_CHAR' [-Wunused-const-variable] static const char TAB_CHAR = '\t'; ^ - Building in src/intersectFile * compiling intersectMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' intersectMain.cpp:12:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from intersectMain.cpp:14: ./intersectFile.h:15:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from intersectMain.cpp:14: In file included from ./intersectFile.h:17: ../utils//FileRecordTools/Records/RecordKeyList.h:14:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from intersectMain.cpp:14: In file included from ./intersectFile.h:17: In file included from ../utils//FileRecordTools/Records/RecordKeyList.h:16: ../utils//FileRecordTools/Records/Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from intersectMain.cpp:14: In file included from ./intersectFile.h:17: In file included from ../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../utils//FileRecordTools/Records/Record.h:13: ../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ - Building in src/jaccard * compiling jaccardMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling RollingBuffer_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 1 warning generated. * compiling TcpSocketEngine_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling intersectFile.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from intersectFile.cpp:13: ./intersectFile.h:15:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from intersectFile.cpp:13: In file included from ./intersectFile.h:17: ../utils//FileRecordTools/Records/RecordKeyList.h:14:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from intersectFile.cpp:13: In file included from ./intersectFile.h:17: In file included from ../utils//FileRecordTools/Records/RecordKeyList.h:16: ../utils//FileRecordTools/Records/Record.h:8:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from intersectFile.cpp:13: In file included from ./intersectFile.h:17: In file included from ../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../utils//FileRecordTools/Records/Record.h:13: ../utils//general/FreeList.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ - Building in src/linksBed * compiling linksMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from intersectMain.cpp:14: In file included from ./intersectFile.h:17: In file included from ../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../utils//FileRecordTools/Records/Record.h:15: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling Jaccard.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from jaccardMain.cpp:12: In file included from ./Jaccard.h:15: In file included from ../utils//Contexts/ContextJaccard.h:11: In file included from ../utils//Contexts/ContextIntersect.h:11: In file included from ../utils//Contexts/ContextBase.h:22: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling TcpSocketEngine_unix_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling linksBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from intersectFile.cpp:13: In file included from ./intersectFile.h:17: In file included from ../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../utils//FileRecordTools/Records/Record.h:15: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ 1 warning generated. * compiling TcpSocket_p.cpp 6 warnings generated. - Building in src/maskFastaFromBed clang: warning: argument unused during compilation: '-L/sw/lib' * compiling maskFastaFromBedMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling SamFormatParser_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling maskFastaFromBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from intersectFile.cpp:13: ./intersectFile.h:35:10: warning: private field '_queryRec' is not used [-Wunused-private-field] Record *_queryRec; ^ ./intersectFile.h:36:10: warning: private field '_databaseRec' is not used [-Wunused-private-field] Record *_databaseRec; ^ 7 warnings generated. * compiling SamFormatPrinter_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from Jaccard.cpp:13: In file included from ./Jaccard.h:15: In file included from ../utils//Contexts/ContextJaccard.h:11: In file included from ../utils//Contexts/ContextIntersect.h:11: In file included from ../utils//Contexts/ContextBase.h:22: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ - Building in src/mapFile * compiling mapMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' mapMain.cpp:12:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ In file included from mapMain.cpp:14: ./mapFile.h:15:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 1 warning generated. * compiling SamHeaderValidator_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling mapFile.cpp * compiling BamException_p.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from mapFile.cpp:12: ./mapFile.h:15:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/mergeFile * compiling mergeMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from mapMain.cpp:14: In file included from ./mapFile.h:20: In file included from ../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../utils//FileRecordTools/Records/Record.h:15: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ - Building in src/multiBamCov * compiling multiBamCovMain.cpp * compiling mergeFile.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/multiIntersectBed * compiling multiIntersectBedMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling multiBamCov.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 3 warnings generated. * compiling multiIntersectBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from mapFile.cpp:12: In file included from ./mapFile.h:20: In file included from ../utils//FileRecordTools/Records/RecordKeyList.h:16: In file included from ../utils//FileRecordTools/Records/Record.h:15: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ In file included from mergeMain.cpp:12: In file included from ./mergeFile.h:20: In file included from ../utils//Contexts/ContextMerge.h:11: In file included from ../utils//Contexts/ContextBase.h:22: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * linking lib/libbamtools.a ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o In file included from mergeFile.cpp:12: In file included from ./mergeFile.h:20: In file included from ../utils//Contexts/ContextMerge.h:11: In file included from ../utils//Contexts/ContextBase.h:22: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ mapFile.cpp:19:11: warning: unused variable 'PRECISION' [-Wunused-const-variable] const int PRECISION = 21; ^ 3 warnings generated. - Building in src/nekSandbox1 * compiling nekSandboxMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 1 warning generated. nekSandboxMain.cpp:1:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ - Building in src/pairToBed - Building in src/nucBed * compiling nucBedMain.cpp * compiling pairToBedMain.cpp ranlib lib/libbamtools.a clang: warning: argument unused during compilation: '-L/sw/lib'clang: warning: argument unused during compilation: '-L/sw/lib' * compiling nucBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 1 warning generated. * compiling pairToBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/pairToPair * compiling pairToPairMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/randomBed * compiling randomBedMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from nekSandboxMain.cpp:3: In file included from ../utils//Contexts/ContextIntersect.h:11: In file included from ../utils//Contexts/ContextBase.h:22: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling pairToPair.cpp 2 warnings generated. clang: warning: argument unused during compilation: '-L/sw/lib' * compiling randomBed.cpp - Building in src/regressTest clang: warning: argument unused during compilation: '-L/sw/lib' compiling RegressTest.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from RegressTest.cpp:1: ./RegressTest.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ - Building in src/reldist * compiling reldistMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling reldist.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/sampleFile * compiling sampleMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/shuffleBed * compiling shuffleBedMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from RegressTest.cpp:3: In file included from ../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:13: In file included from ../utils//FileRecordTools/FileReaders/FileReader.h:12: In file included from ../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:15: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling SampleFile.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from SampleFile.cpp:8: ./SampleFile.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ * compiling shuffleBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/slopBed * compiling slopBedMain.cpp In file included from sampleMain.cpp:9: In file included from ../utils//Contexts/ContextSample.h:11: In file included from ../utils//Contexts/ContextBase.h:22: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/sortBed * compiling sortMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from SampleFile.cpp:8: In file included from ./SampleFile.h:13: In file included from ../utils//Contexts/ContextSample.h:11: In file included from ../utils//Contexts/ContextBase.h:22: ../utils//fileType/FileRecordTypeChecker.h:120:21: warning: in-class initializer for static data member of type 'const float' is a GNU extension [-Wgnu-static-float-init] static const float PERCENTAGE_PRINTABLE = .9; ^ ~~ * compiling slopBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' 1 warning generated. - Building in src/subtractBed * compiling subtractMain.cpp 2 warnings generated. compiling regressTestMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' In file included from regressTestMain.cpp:2: ./RegressTest.h:11:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ * compiling sortBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' In file included from SampleFile.cpp:8: ./SampleFile.h:35:6: warning: private field '_seed' is not used [-Wunused-private-field] int _seed; ^ 3 warnings generated. * compiling subtractBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/tagBam * compiling tagBamMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/unionBedGraphs * compiling unionBedGraphsMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling tagBam.cpp 1 warning generated. * compiling unionBedGraphs.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' - Building in src/windowBed * compiling windowMain.cpp clang: warning: argument unused during compilation: '-L/sw/lib' * compiling windowBed.cpp clang: warning: argument unused during compilation: '-L/sw/lib' subtractBed.cpp:126:29: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((numConsumedByB == 0)) { ~~~~~~~~~~~~~~~^~~~ subtractBed.cpp:126:29: note: remove extraneous parentheses around the comparison to silence this warning if ((numConsumedByB == 0)) { ~ ^ ~ subtractBed.cpp:126:29: note: use '=' to turn this equality comparison into an assignment if ((numConsumedByB == 0)) { ^~ = - Building in src/windowMaker 1 warning generated. * compiling windowMakerMain.cpp * compiling windowMaker.cpp clang: warning: argument unused during compilation: '-L/sw/lib' clang: warning: argument unused during compilation: '-L/sw/lib' - Building main bedtools binary. done. - Creating executables for old CLI. done. make: Leaving directory `/sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1' make -j1 -C docs man sphinx-build -b man -d _build/doctrees . _build/man Making output directory... Running Sphinx v1.2.2 loading pickled environment... not yet created loading intersphinx inventory from http://bedtools.readthedocs.org/en/latest/objects.inv... building [man]: all manpages updating environment: 50 added, 0 changed, 0 removed reading sources... [ 2%] content/advanced-usage reading sources... [ 4%] content/bedtools-suite reading sources... [ 6%] content/example-usage reading sources... [ 8%] content/faq reading sources... [ 10%] content/general-usage reading sources... [ 12%] content/history reading sources... [ 14%] content/installation reading sources... [ 16%] content/overview reading sources... [ 18%] content/quick-start reading sources... [ 20%] content/related-tools reading sources... [ 22%] content/tips-and-tricks reading sources... [ 24%] content/tools/annotate reading sources... [ 26%] content/tools/bamtobed reading sources... [ 28%] content/tools/bamtofastq reading sources... [ 30%] content/tools/bed12tobed6 reading sources... [ 32%] content/tools/bedpetobam reading sources... [ 34%] content/tools/bedtobam reading sources... [ 36%] content/tools/closest reading sources... [ 38%] content/tools/cluster reading sources... [ 40%] content/tools/complement reading sources... [ 42%] content/tools/coverage reading sources... [ 44%] content/tools/expand reading sources... [ 46%] content/tools/flank reading sources... [ 48%] content/tools/genomecov reading sources... [ 50%] content/tools/getfasta reading sources... [ 52%] content/tools/groupby reading sources... [ 54%] content/tools/igv reading sources... [ 56%] content/tools/intersect reading sources... [ 58%] content/tools/jaccard reading sources... [ 60%] content/tools/links reading sources... [ 62%] content/tools/makewindows reading sources... [ 64%] content/tools/map reading sources... [ 66%] content/tools/maskfasta reading sources... [ 68%] content/tools/merge reading sources... [ 70%] content/tools/multicov reading sources... [ 72%] content/tools/multiinter reading sources... [ 74%] content/tools/nuc reading sources... [ 76%] content/tools/overlap reading sources... [ 78%] content/tools/pairtobed reading sources... [ 80%] content/tools/pairtopair reading sources... [ 82%] content/tools/random reading sources... [ 84%] content/tools/reldist reading sources... [ 86%] content/tools/shuffle reading sources... [ 88%] content/tools/slop reading sources... [ 90%] content/tools/sort reading sources... [ 92%] content/tools/subtract reading sources... [ 94%] content/tools/tag reading sources... [ 96%] content/tools/unionbedg reading sources... [ 98%] content/tools/window reading sources... [100%] index /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/history.rst:15: WARNING: Enumerated list ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/history.rst:18: WARNING: Block quote ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/history.rst:20: WARNING: Enumerated list ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/history.rst:23: WARNING: Block quote ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/related-tools.rst:3: WARNING: Duplicate explicit target name: "here". /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/cluster.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/intersect.rst:74: WARNING: Block quote ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/merge.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/merge.rst:230: WARNING: Explicit markup ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/merge.rst:236: WARNING: Explicit markup ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/merge.rst:242: WARNING: Explicit markup ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/pairtopair.rst:30: WARNING: Block quote ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/random.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/random.rst:None: WARNING: image file not readable: content/tools/../images/tool-glyphs/random-glyph.png looking for now-outdated files... none found pickling environment... done checking consistency... done writing... bedtools.1 { content/overview content/installation content/quick-start content/general-usage content/history content/bedtools-suite content/tools/annotate content/tools/bamtobed content/tools/bamtofastq content/tools/bed12tobed6 content/tools/bedpetobam content/tools/bedtobam content/tools/closest content/tools/cluster content/tools/complement content/tools/coverage content/tools/expand content/tools/flank content/tools/genomecov content/tools/getfasta content/tools/groupby content/tools/igv content/tools/intersect content/tools/jaccard content/tools/links content/tools/makewindows content/tools/map content/tools/maskfasta content/tools/merge content/tools/multicov content/tools/multiinter content/tools/nuc content/tools/overlap content/tools/pairtobed content/tools/pairtopair content/tools/random content/tools/reldist content/tools/shuffle content/tools/slop content/tools/sort content/tools/subtract content/tools/tag content/tools/unionbedg content/tools/window content/example-usage content/advanced-usage content/tips-and-tricks content/faq content/related-tools } build succeeded, 14 warnings. Build finished. The manual pages are in _build/man. make -j1 -C docs html sphinx-build -b html -d _build/doctrees . _build/html Making output directory... Running Sphinx v1.2.2 loading pickled environment... done building [html]: targets for 50 source files that are out of date updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] content/tools/random /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/random.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent. /sw/build.build/bedtools-2.20.1-2/bedtools2-2.20.1/docs/content/tools/random.rst:None: WARNING: image file not readable: content/tools/../images/tool-glyphs/random-glyph.png looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... WARNING: html_favicon is not an .ico file done writing output... [ 2%] content/advanced-usage writing output... [ 4%] content/bedtools-suite writing output... [ 6%] content/example-usage writing output... [ 8%] content/faq writing output... [ 10%] content/general-usage writing output... [ 12%] content/history writing output... [ 14%] content/installation writing output... [ 16%] content/overview writing output... [ 18%] content/quick-start writing output... [ 20%] content/related-tools writing output... [ 22%] content/tips-and-tricks writing output... [ 24%] content/tools/annotate writing output... [ 26%] content/tools/bamtobed writing output... [ 28%] content/tools/bamtofastq writing output... [ 30%] content/tools/bed12tobed6 writing output... [ 32%] content/tools/bedpetobam writing output... [ 34%] content/tools/bedtobam writing output... [ 36%] content/tools/closest writing output... [ 38%] content/tools/cluster writing output... [ 40%] content/tools/complement writing output... [ 42%] content/tools/coverage writing output... [ 44%] content/tools/expand writing output... [ 46%] content/tools/flank writing output... [ 48%] content/tools/genomecov writing output... [ 50%] content/tools/getfasta writing output... [ 52%] content/tools/groupby writing output... [ 54%] content/tools/igv writing output... [ 56%] content/tools/intersect writing output... [ 58%] content/tools/jaccard writing output... [ 60%] content/tools/links writing output... [ 62%] content/tools/makewindows writing output... [ 64%] content/tools/map writing output... [ 66%] content/tools/maskfasta writing output... [ 68%] content/tools/merge writing output... [ 70%] content/tools/multicov writing output... [ 72%] content/tools/multiinter writing output... [ 74%] content/tools/nuc writing output... [ 76%] content/tools/overlap writing output... [ 78%] content/tools/pairtobed writing output... [ 80%] content/tools/pairtopair writing output... [ 82%] content/tools/random writing output... [ 84%] content/tools/reldist writing output... [ 86%] content/tools/shuffle writing output... [ 88%] content/tools/slop writing output... [ 90%] content/tools/sort writing output... [ 92%] content/tools/subtract writing output... [ 94%] content/tools/tag writing output... [ 96%] content/tools/unionbedg writing output... [ 98%] content/tools/window writing output... [100%] index writing additional files... (0 module code pages) genindex search copying images... [ 4%] content/tools/../images/tool-glyphs/merge-glyph.png copying images... [ 9%] content/tools/../images/tool-glyphs/map-glyph.png copying images... [ 13%] content/images/github-zip-button.png copying images... [ 18%] content/images/speed-comparo.png copying images... [ 22%] content/tools/../images/tool-glyphs/jaccard-glyph.png copying images... [ 27%] content/tools/../images/tool-glyphs/subtract-glyph.png copying images... [ 31%] content/images/bedtoolsMenu.png copying images... [ 36%] content/tools/../images/tool-glyphs/intersect-glyph.png copying images... [ 40%] content/tools/../images/tool-glyphs/complement-glyph.png copying images... [ 45%] content/tools/../images/tool-glyphs/reldist-glyph.png copying images... [ 50%] content/tools/../images/tool-glyphs/cluster-glyph.png copying images... [ 54%] content/tools/../images/tool-glyphs/map-speed-comparo.png copying images... [ 59%] content/tools/../images/tool-glyphs/slop-glyph.png copying images... [ 63%] content/images/galaxy-bedtools.png copying images... [ 68%] content/tools/../images/tool-glyphs/genomecov-glyph.png copying images... [ 72%] content/tools/../images/tool-glyphs/flank-glyph.png copying images... [ 77%] content/tools/../images/tool-glyphs/shuffle-glyph.png copying images... [ 81%] content/images/memory-comparo.png copying images... [ 86%] content/tools/../images/tool-glyphs/window-glyph.png copying images... [ 90%] content/tools/../images/tool-glyphs/getfasta-glyph.png copying images... [ 95%] content/tools/../images/tool-glyphs/reldist-plot.png copying images... [100%] content/tools/../images/tool-glyphs/maskfasta-glyph.png copying static files... done copying extra files... done dumping search index... done dumping object inventory... done build succeeded, 3 warnings. Build finished. The HTML pages are in _build/html. /bin/rm -rf /sw/build.build/root-bedtools-2.20.1-2 /bin/mkdir -p /sw/build.build/root-bedtools-2.20.1-2/sw /bin/mkdir -p /sw/build.build/root-bedtools-2.20.1-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bedtools-2.20.1-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.5YpHI install -m 755 -d /sw/build.build/root-bedtools-2.20.1-2/sw/bin install -m 755 -d /sw/build.build/root-bedtools-2.20.1-2/sw/share/man/man1 install -m 755 -d /sw/build.build/root-bedtools-2.20.1-2/sw/share/doc/bedtools cp bin/* /sw/build.build/root-bedtools-2.20.1-2/sw/bin/ cp docs/_build/man/bedtools.1 /sw/build.build/root-bedtools-2.20.1-2/sw/share/man/man1 cp -R docs/_build/html /sw/build.build/root-bedtools-2.20.1-2/sw/share/doc/bedtools sudo -u fink-bld [ENV] sh -c /tmp/fink.DUYCC /usr/bin/install -d -m 700 /sw/build.build/root-bedtools-2.20.1-2/sw/share/doc/bedtools /bin/cp -r LICENSE /sw/build.build/root-bedtools-2.20.1-2/sw/share/doc/bedtools/ /bin/cp -r README.md /sw/build.build/root-bedtools-2.20.1-2/sw/share/doc/bedtools/ /bin/cp -r RELEASE_HISTORY /sw/build.build/root-bedtools-2.20.1-2/sw/share/doc/bedtools/ /bin/chmod -R go=u-w /sw/build.build/root-bedtools-2.20.1-2/sw/share/doc/bedtools /bin/rm -f /sw/build.build/root-bedtools-2.20.1-2/sw/info/dir /sw/build.build/root-bedtools-2.20.1-2/sw/info/dir.old /sw/build.build/root-bedtools-2.20.1-2/sw/share/info/dir /sw/build.build/root-bedtools-2.20.1-2/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-bedtools-2.20.1-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `bedtools' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/bedtools_2.20.1-2_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bedtools-2.20.1-2 (Reading database ... 16279 files and directories currently installed.) Removing fink-buildlock-bedtools-2.20.1-2 ...