Merge branch 'release/v1.7.0'

CHANGES.md

@@ -1,91 +1,119 @@
-1.6.0
-  * Adding local file mode for sites that cannot download from GNOS when the xml_to_bas.pl script runs
-  * [gnos_pull.pl](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/wiki/Scripts-PanCancer-Specific#gnos_pullpl) - see linked docs
-1.5.4
-  bam_stats C
-  * Reference file parameter is now optional to replicate bam_stats.pl functionality.
-  * Warnings in help, and when a cram file is given as reference from header may not be found, and bam stats will fail.
-1.5.3
-  bam_stats C - changed array for khash in insert size calculations in order to make code more robust.
-  Header RG line reading now reads anything not a tab or newline as it should when determining what the values of tags are.
-1.5.2
-  bamToBw.pl fixes
-  * Pull actual binaries from jkent_util not html page associated
-  * process name corrections in bamToBw.pm command line args
-1.5.1
-  bam_stats c now has CRAM support.
-  Also dropped need for samtools v1.x api as can be handled by htslib on it's own.
-1.5.0
-  bamToBw.pl and new biobambam dep
-  No changes to old tools, just additions and prep for handling CRAM input.
-1.4.0
-  bam_stats in C, less than 2 hours to generate stats on a sample level BAM file of ~120GB.
-1.3.0
-  bam_stats.pl is now multi-threaded, can get ~50% runtime reduction with 3-4 threads, memory still <500MB.
-  Upgrades biobambam to 0.0.185 (and dependencies).
-1.2.3
-  xml_to_bas.pl - detect readgroup id clashes and attempt to reconcile, #54
-1.2.2
-  Fixed bug in bwa_mem.pl when using '-f' option on paired fastq.
-1.2.1
-  Makes xml_to_bas.pl more robust on AWS. Retrieved XML was being truncated on some network configurations.
-1.2.0
-  Modifications made to the bwa_mem.pl code to split a lane of data into fragments to reduce failure recovery time. Primarily added to handle X10 data better.
-  Also updated samtools to 0.1.20, last version that is currently compatible with Bio::DB::Sam.
-1.1.1
-  Fix missing dependancy and build a relocatable version of biobambam suitable for use in artifactory.
-1.1.0
-  Minor enhancement to bwa_mem.pl to automatically generate the *.bas file.
-  Added xml_to_bas.pl for pancancer users, see the wiki for details.
-  Fixed a few minor issues, #36, #37, #39
-1.0.4
-  Install biobambam 0.0.142 to prevent over-counting of duplicates when multiple
-  libraries, also required libmaus 0.0.124.
-  Improve install for those working with multiple perl installs.
-  Improve version inheritance, less code
-1.0.3
-  Corrected issue from dynamic de-reference of hash, issue fort pre 5.14 perl
-  and potentially unstable in future.
-  Added missing project code to cv terms.
-  Bug-fixed upgrade path, still needs better solution.
-  Cleaned up messaging in Threaded module.
-1.0.2
-  Upgrade install to pull biobambam 0.0.138
-   - fastqtobam option 'pairedfile' for where readnames don't have trailing '/1' or '/2'.
-   - fastqtobam option to relax qscore validation without turning off... careful
-  Upgrade install to pull BWA 0.7.8
-   - performance improvements for short read alignment (100bp)
-1.0.1
-  Upgrade install to pull biobambam 0.0.135
-    - fastqtobam supports Casava v1.8
-    - bamsort supports NM/MD correction during sam->bam/merge process
-  Minor enhancement to BAS reader module
-  Sample name from command line passed through to SM of RG header in bwa_mem.pl
-  SRA.pm - check that rg id is unique within run of code (thanks to Junjun Zhang)
-  Threads.pm - join interval is now configurable.
-1.0.0
-  bam_stats.pl actually installed now.
-  Basic *.bas perl access module.
-  Upgraded libmaus/biobambam to resolve patch and CentOS install issue.
-  Reference implementations ensure unique RG:ID between files.
-0.3.0
-  Changes for the re-worked PanCancer submission SOP.
-  Patch for libmaus issue as not going to be a release in time.
-  Bug fix for *.info files (bam_to_sra_sub.pl).
-  Added bam_stats.pl.
-  Project is now defaulted when not provided (bam_to_sra_sub.pl).
-0.2.0 14-Mar-2014
-  Updated biobambam version
-  Documented additional dependencies
-  Improved install implementation
-0.0.2-beta2 04-Feb-2014
-  Updated module naming in preparation for publication to GitHub.
-  Added license boiler plate.
-  bam_to_sra_sub.pl generates valid XML for GNOS, some features disabled
-  until modifications to GNOS can be made (warnings indicate this on execution)
-0.0.2-beta 29-Jan-2014
-  Pre release with basic SRA XML generation (GENOS)
-  Updated requirements for biobambam of 0.0.120
-  Tests update to reflect change in biobambam requirement
-0.0.1 11-Sep-2013
-  Initial codebase for PanCancer alignment with BWA 0.6.2.
+### 1.7.0
+* Switched to bam_stats C in ``bwa_mem.pl``.
+* Updates to ``bam_to_sra.pl`` to prevent bad SM values in unaligned BAM uploads.
+
+### 1.6.0
+* Adding local file mode for sites that cannot download from GNOS when the xml_to_bas.pl script runs
+* [gnos_pull.pl](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/wiki/Scripts-PanCancer-Specific#gnos_pullpl) - see linked docs
+
+### 1.5.4
+* bam_stats C
+    * Reference file parameter is now optional to replicate bam_stats.pl functionality.
+    * Warnings in help, and when a cram file is given as reference from header may not be found, and bam stats will fail.
+
+### 1.5.3
+* bam_stats C - changed array for khash in insert size calculations in order to make code more robust.
+* Header RG line reading now reads anything not a tab or newline as it should when determining what the values of tags are.
+
+### 1.5.2
+bamToBw.pl fixes
+* Pull actual binaries from jkent_util not html page associated
+* process name corrections in bamToBw.pm command line args
+
+### 1.5.1
+* bam_stats c now has CRAM support.
+* Also dropped need for samtools v1.x api as can be handled by htslib on it's own.
+
+### 1.5.0
+* bamToBw.pl and new biobambam dep
+
+No changes to old tools, just additions and prep for handling CRAM input.
+
+### 1.4.0
+bam_stats in C, less than 2 hours to generate stats on a sample level BAM file of ~120GB.
+
+### 1.3.0
+* bam_stats.pl is now multi-threaded, can get ~50% runtime reduction with 3-4 threads, memory still <500MB.
+* Upgrades biobambam to 0.0.185 (and dependencies).
+
+### 1.2.3
+xml_to_bas.pl - detect readgroup id clashes and attempt to reconcile, #54
+
+### 1.2.2
+Fixed bug in bwa_mem.pl when using '-f' option on paired fastq.
+
+### 1.2.1
+Makes xml_to_bas.pl more robust on AWS. Retrieved XML was being truncated on some network configurations.
+
+### 1.2.0
+Modifications made to the bwa_mem.pl code to split a lane of data into fragments to reduce failure recovery time. Primarily added to handle X10 data better.
+
+Also updated samtools to 0.1.20, last version that is currently compatible with Bio::DB::Sam.
+
+### 1.1.1
+Fix missing dependancy and build a relocatable version of biobambam suitable for use in artifactory.
+
+### 1.1.0
+* Minor enhancement to bwa_mem.pl to automatically generate the *.bas file.
+* Added xml_to_bas.pl for pancancer users, see the wiki for details.
+* Fixed a few minor issues, #36, #37, #39
+
+### 1.0.4
+* Install biobambam 0.0.142 to prevent over-counting of duplicates when multiple
+libraries, also required libmaus 0.0.124.
+* Improve install for those working with multiple perl installs.
+* Improve version inheritance, less code
+
+### 1.0.3
+* Corrected issue from dynamic de-reference of hash, issue for pre 5.14 perl
+and potentially unstable in future.
+* Added missing project code to cv terms.
+* Bug-fixed upgrade path, still needs better solution.
+* Cleaned up messaging in Threaded module.
+
+### 1.0.2
+* Upgrade install to pull biobambam 0.0.138
+    * fastqtobam option 'pairedfile' for where readnames don't have trailing '/1' or '/2'.
+    * fastqtobam option to relax qscore validation without turning off... careful
+* Upgrade install to pull BWA 0.7.8
+    * performance improvements for short read alignment (100bp)
+
+### 1.0.1
+* Upgrade install to pull biobambam 0.0.135
+    * fastqtobam supports Casava v1.8
+    * bamsort supports NM/MD correction during sam->bam/merge process
+* Minor enhancement to BAS reader module.
+* Sample name from command line passed through to SM of RG header in bwa_mem.pl
+* SRA.pm - check that rg id is unique within run of code (thanks to Junjun Zhang)
+* Threads.pm - join interval is now configurable.
+
+### 1.0.0
+* bam_stats.pl actually installed now.
+* Basic *.bas perl access module.
+* Upgraded libmaus/biobambam to resolve patch and CentOS install issue.
+* Reference implementations ensure unique RG:ID between files.
+
+### 0.3.0
+* Changes for the re-worked PanCancer submission SOP.
+* Patch for libmaus issue as not going to be a release in time.
+* Bug fix for *.info files (bam_to_sra_sub.pl).
+* Added bam_stats.pl.
+* Project is now defaulted when not provided (bam_to_sra_sub.pl).
+
+### 0.2.0 14-Mar-2014
+* Updated biobambam version
+* Documented additional dependencies
+* Improved install implementation
+
+### 0.0.2-beta2 04-Feb-2014
+* Updated module naming in preparation for publication to GitHub.
+* Added license boiler plate.
+* bam_to_sra_sub.pl generates valid XML for GNOS, some features disabled until modifications to GNOS can be made (warnings indicate this on execution)
+
+### 0.0.2-beta 29-Jan-2014
+* Pre release with basic SRA XML generation (GENOS)
+* Updated requirements for biobambam of 0.0.120
+* Tests update to reflect change in biobambam requirement
+
+### 0.0.1 11-Sep-2013
+* Initial codebase for PanCancer alignment with BWA 0.6.2.

MYMETA.json

@@ -57,5 +57,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.6.3"
+   "version" : "v1.7.0"
 }

MYMETA.yml

@@ -39,4 +39,4 @@ requires:
   Test::Fatal: '0.013'
   Try::Tiny: '0.19'
   XML::Simple: '2.2'
-version: v1.6.3
+version: v1.7.0

c/Makefile

@@ -1,4 +1,4 @@
-VERSION=1.6.3
+VERSION=1.7.0
 
 #Compiler
 CC = gcc -O3 -DVERSION='"$(VERSION)"' -g

lib/PCAP.pm

@@ -24,7 +24,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.6.3';
+our $VERSION = '1.7.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>
@@ -63,6 +63,7 @@ const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,bwa,samtools',
                             '1.6.1'  => '',
                             '1.6.2'  => '',
                             '1.6.3'  => '',
+                            '1.7.0'  => '',
                           );
 
 sub license {

lib/PCAP/Bam.pm

@@ -134,7 +134,7 @@ sub bam_stats {
   my $bam = File::Spec->catdir($options->{'outdir'}, $options->{'sample'}).'.bam';;
   my $bas = "$bam.bas";
   my $command = "$^X ";
-  $command .= _which('bam_stats.pl') || die "Unable to find 'bam_stats.pl' in path";
+  $command .= _which('bam_stats') || die "Unable to find 'bam_stats' in path";
   $command .= sprintf $BAM_STATS, $bam, $bas;
   if(exists $options->{'charts'} && defined $options->{'charts'}) {
     my $chart_dir = File::Spec->catdir($options->{'outdir'}, 'charts');

lib/PCAP/SRA.pm

@@ -307,12 +307,20 @@ sub parse_input {
     for my $tag(@REQUIRED_HEADER_TAGS) {
       $bam_detail{$tag} = $bam->single_rg_value($tag);
       if($tag eq 'SM') {
-        my $sm = lc $bam_detail{$tag};
+        my $sm = $bam_detail{$tag};
         if($sm =~ /^([a-f0-9]{8})([a-f0-9]{4})([a-f0-9]{4})([a-f0-9]{4})([a-f0-9]{12})$/) {
           $sm = join q{-}, ($1,$2,$3,$4,$5);
         }
+        # check after format change
+        unless($sm =~ /^([a-f0-9]{8})-([a-f0-9]{4})-([a-f0-9]{4})-([a-f0-9]{4})-([a-f0-9]{12})$/) {
+          croak sprintf 'SM tag is not a lowercase UUID: %s (%s)', $bam_detail{$tag}, $file;
+        }
         $bam_detail{$tag} = $sm;
       }
+
+      if($tag eq 'PL' && $bam_detail{$tag} ne 'ILLUMINA') {
+        croak sprintf 'PanCancer WGS only supports ILLUMINA as a value for PL: %s ($s)', $bam_detail{$tag}, $file;
+      }
     }
     $bam_detail{'file'} = $bam->{'bam'};
     $bam_detail{'md5'} = $bam->{'md5'};