release files

Author: keiranmraine

MANIFEST

@@ -1,29 +1,4 @@
 .travis.yml
-bam_out/logs_bwamem_wibble/PCAP_Bam_merge_and_mark_dup.0.err
-bam_out/logs_bwamem_wibble/PCAP_Bam_merge_and_mark_dup.0.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.1.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.1.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.2.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.2.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.3.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.3.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.4.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.4.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.5.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.5.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.6.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.6.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.7.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.7.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.8.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.8.out
-bam_out/logs_bwamem_wibble/PCAP_Bwa_split_in.1.err
-bam_out/logs_bwamem_wibble/PCAP_Bwa_split_in.1.out
-bam_out/wibble.bam
-bam_out/wibble.bam.bai
-bam_out/wibble.bam.bas
-bam_out/wibble.bam.md5
-bam_out/wibble.bam.met
 bin/bam_stats.pl
 bin/bam_to_sra_sub.pl
 bin/bamToBw.pl
@@ -49,116 +24,14 @@ c/c_tests/minunit.h
 c/c_tests/runtests.sh
 c/c_tests/tests_log
 c/dbg.h
+c/diff_bams.c
 c/khash.h
 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
-fastq/1/10658_1.fq.gz
-fastq/1/10659_1.fq.gz
-fastq/1/10660_1.fq.gz
-fastq/1/10661_1.fq.gz
-fastq/1/10662_1.fq.gz
-fastq/1/10663_1.fq.gz
-fastq/1/10664_1.fq.gz
-fastq/1/10665_1.fq.gz
-fastq/2/10658_2.fq.gz
-fastq/2/10659_2.fq.gz
-fastq/2/10660_2.fq.gz
-fastq/2/10661_2.fq.gz
-fastq/2/10662_2.fq.gz
-fastq/2/10663_2.fq.gz
-fastq/2/10664_2.fq.gz
-fastq/2/10665_2.fq.gz
-fastq_i/10658_i.fq.gz
-fastq_i/10659_i.fq.gz
-fastq_i/10660_i.fq.gz
-fastq_i/10661_i.fq.gz
-fastq_i/10662_i.fq.gz
-fastq_i/10663_i.fq.gz
-fastq_i/10664_i.fq.gz
-fastq_i/10665_i.fq.gz
-fastq_i_out/logs_bwamem_wibble/PCAP_Bam_merge_and_mark_dup.0.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bam_merge_and_mark_dup.0.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.1.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.1.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.2.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.2.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.3.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.3.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.4.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.4.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.5.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.5.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.6.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.6.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.7.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.7.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.8.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.8.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.1.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.1.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.2.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.2.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.3.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.3.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.4.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.4.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.5.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.5.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.6.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.6.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.7.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.7.out
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.8.err
-fastq_i_out/logs_bwamem_wibble/PCAP_Bwa_split_in.8.out
-fastq_i_out/wibble.bam
-fastq_i_out/wibble.bam.bai
-fastq_i_out/wibble.bam.bas
-fastq_i_out/wibble.bam.md5
-fastq_i_out/wibble.bam.met
-fastq_out/logs_bwamem_wibble/PCAP_Bam_merge_and_mark_dup.0.err
-fastq_out/logs_bwamem_wibble/PCAP_Bam_merge_and_mark_dup.0.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.1.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.1.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.2.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.2.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.3.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.3.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.4.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.4.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.5.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.5.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.6.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.6.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.7.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.7.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.8.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_bwa_mem.8.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.1.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.1.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.2.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.2.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.3.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.3.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.4.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.4.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.5.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.5.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.6.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.6.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.7.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.7.out
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.8.err
-fastq_out/logs_bwamem_wibble/PCAP_Bwa_split_in.8.out
-fastq_out/wibble.bam
-fastq_out/wibble.bam.bai
-fastq_out/wibble.bam.bas
-fastq_out/wibble.bam.md5
-fastq_out/wibble.bam.met
-insilico_21.bam
 INSTALL.md
 lib/PCAP.pm
 lib/PCAP/Bam.pm