Finalised release

ICGC-TCGA-PanCancer · Oct 13, 2016 · bd4700a · bd4700a
1 parent 0127a81
commit bd4700a
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Showing 3 changed files with 2 additions and 50 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -10,15 +10,13 @@ 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
 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
diff --git 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 {