diff --git a/MANIFEST b/MANIFEST index a1775d1..bec8c9e 100644 --- a/MANIFEST +++ b/MANIFEST @@ -10,7 +10,6 @@ bin/gnos_pull.pl bin/monitor.pl bin/xam_coverage_bins.pl bin/xml_to_bas.pl -c/bam2bedgraph.c c/bam_access.c c/bam_access.h c/bam_stats.c @@ -18,7 +17,6 @@ c/bam_stats_calcs.c c/bam_stats_calcs.h c/bam_stats_output.c c/bam_stats_output.h -c/bwcat.c 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 diff --git a/docs.tar.gz b/docs.tar.gz index 5f16ef7..30b61e0 100644 Binary files a/docs.tar.gz and b/docs.tar.gz differ diff --git a/lib/PCAP.pm b/lib/PCAP.pm index ed44ca3..f31480c 100644 --- a/lib/PCAP.pm +++ b/lib/PCAP.pm @@ -27,7 +27,7 @@ use FindBin qw($Bin); use File::Which qw(which); # don't use autodie, only core perl in here -our $VERSION = '3.1.1'; +our $VERSION = '3.2.0'; our @EXPORT = qw($VERSION _which); const my $LICENSE => @@ -38,53 +38,7 @@ const my $LICENSE => #################"; const my $DEFAULT_PATH => 'biobambam,samtools,bwa'; -const my %UPGRADE_PATH => ( # all earlier versions need full upgrade - '1.2.0' => 'biobambam,samtools,bwa', # if later versions have new versions then all preceding need that tool listing - '1.2.1' => 'biobambam,samtools,bwa', - '1.2.2' => 'biobambam,samtools,bwa', - '1.3.0' => 'biobambam,samtools,bwa', - '1.4.0' => 'biobambam,samtools,bwa', - '1.5.0' => 'biobambam,samtools,bwa', - '1.5.1' => 'biobambam,samtools,bwa', - '1.5.2' => 'biobambam,samtools,bwa', - '1.5.3' => 'biobambam,samtools,bwa', - '1.5.4' => 'biobambam,samtools,bwa', - '1.6.0' => 'biobambam,samtools,bwa', - '1.6.1' => 'biobambam,samtools,bwa', - '1.6.2' => 'biobambam,samtools,bwa', - '1.6.3' => 'biobambam,samtools,bwa', - '1.7.0' => 'biobambam,samtools,bwa', - '1.7.1' => 'biobambam,samtools,bwa', - '1.8.0' => 'biobambam,samtools', - '1.8.1' => 'biobambam,samtools', - '1.8.2' => 'biobambam,samtools', - '1.9.0' => 'biobambam,samtools', - '1.9.1' => 'biobambam,samtools', - '1.9.4' => 'biobambam,samtools', - '1.10.0' => 'biobambam,samtools', - '1.11.0' => 'biobambam,samtools', - '1.11.1' => 'biobambam,samtools', - '1.12.0' => 'biobambam,samtools', - '1.12.1' => 'biobambam,samtools', - '1.12.2' => 'biobambam,samtools', - '1.12.3' => 'biobambam,samtools', - '1.13.0' => 'biobambam,samtools', - '1.13.1' => 'biobambam,samtools', - '1.13.2' => 'biobambam,samtools', - '1.14.0' => 'biobambam,samtools', - '2.0.0' => 'biobambam', - '2.0.1' => 'biobambam,samtools', - '2.1.0' => 'biobambam,samtools', - '2.1.2' => 'biobambam,samtools', - '2.1.3' => 'biobambam,samtools', - '2.2.0' => 'biobambam,samtools', - '2.2.1' => 'biobambam', - '2.3.0' => 'biobambam', - '2.4.0' => 'biobambam', - '2.5.0' => 'biobambam', - '3.0.0' => '', - '3.1.0' => '', - '3.1.1' => '', +const my %UPGRADE_PATH => ( # just always install, it's safer ); sub license {