MANIFEST

.travis.yml
bin/bamToBw.pl
bin/bwa_aln.pl
bin/bwa_mem.pl
bin/xam_coverage_bins.pl
c/bam_access.c
c/bam_access.h
c/bam_stats.c
c/bam_stats_calcs.c
c/bam_stats_calcs.h
c/bam_stats_output.c
c/bam_stats_output.h
c/c_tests/01_bam_stats_output_tests.c
c/c_tests/02_bam_access_tests.c
c/c_tests/03_bam_stats_calcs_tests.c
c/c_tests/minunit.h
c/c_tests/runtests.sh
c/c_tests/test_04_mismatchQc.sh
c/c_tests/tests_log
c/dbg.h
c/diff_bams.c
c/khash.h
c/mismatchQc.c
c/reheadSQ.c
CHANGES.md
dists/patch/Bio-BigFile_build.patch
dists/snappy-1.1.2.tar.gz
docs.tar.gz
examples/gnos_pull.ini
INSTALL.md
lib/PCAP.pm
lib/PCAP/Bam.pm
lib/PCAP/Bam/Bas.pm
lib/PCAP/Bam/Coverage.pm
lib/PCAP/Bam/Stats.pm
lib/PCAP/BigWig.pm
lib/PCAP/Bwa.pm
lib/PCAP/Bwa/Meta.pm
lib/PCAP/Cli.pm
lib/PCAP/Threaded.pm
LICENSE
Makefile.PL
MANIFEST			This list of files
MANIFEST.SKIP
prerelease.sh
README.md
setup.sh
t/1_pm_compile.t
t/2_pl_compile.t
t/3_external_progs.t
t/data/1.fq
t/data/1_1.fq
t/data/1_2.fq
t/data/2_1.fq
t/data/3_2.fq
t/data/coverage.bam
t/data/coverage.bam.bai
t/data/coverage_exons.bed
t/data/coverage_exons.gff3
t/data/data.file
t/data/empty.bam
t/data/empty.bam.bas
t/data/empty.file
t/data/empty.fq
t/data/empty_r1_1.fq
t/data/empty_r1_2.fq
t/data/empty_r2_1.fq
t/data/empty_r2_2.fq
t/data/good.yaml
t/data/header.bam
t/data/header.sam
t/data/malformed_head.bam
t/data/malformed_head.sam
t/data/md5.bam
t/data/md5.bam.md5
t/data/mismatch_expected_out.sam
t/data/mismatch_expected_out_low_frac.sam
t/data/mismatch_test.bam
t/data/mismatch_test.bam.bai
t/data/multi_sample.bam
t/data/multi_sample.sam
t/data/no_readgroups.bam
t/data/no_readgroups.sam
t/data/not_really_a.bam
t/data/paired.bam
t/data/reconcile_bas.bam
t/data/Stats.bam
t/data/Stats.bam.bas
t/data/Stats.c.bam.bas
t/data/test.bam.bas
t/data/unpaired.bam
t/pcap.t
t/pcapBam.t
t/pcapBamBas.t
t/pcapBwa.t
t/pcapBwaMeta.t
t/pcapCli.t
t/pcapCoverage.t
t/pcapThreaded.t