From 88b383ce8b895bb434607b04cf3a13daaac94dc1 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Thu, 15 Mar 2018 12:35:48 +0000
Subject: [PATCH 1/2] Fix an error in input processing of CRAM

---
 CHANGES.md      | 4 ++++
 lib/PCAP.pm     | 2 +-
 lib/PCAP/Bwa.pm | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 0e13519..38c4edb 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 4.2.1
+
+Fix for input type of CRAM.
+
 ## 4.2.0
 
 * Add threadpool to `bam_stats` and `diff_bams`. Fixes #18, Fixes #19
diff --git a/lib/PCAP.pm b/lib/PCAP.pm
index 71f589d..6bb7f9b 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 = '4.2.0';
+our $VERSION = '4.2.1';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>
diff --git a/lib/PCAP/Bwa.pm b/lib/PCAP/Bwa.pm
index 89c768d..2157dd2 100644
--- a/lib/PCAP/Bwa.pm
+++ b/lib/PCAP/Bwa.pm
@@ -206,7 +206,7 @@ sub split_in {
       my $cmd;
       if($input->bam_or_cram eq 'cram') {
         $cmd = sprintf $CRAMFASTQ, $bam2fq,
-                                  $options->{'reference'},,
+                                  $options->{'reference'},
                                   File::Spec->catfile($tmp, "bamtofastq.$index"),
                                   $split_folder,
                                   $fragment_size * $MILLION * $BAM_MULT,

From e558006d16642372b090f2748f984c3816885556 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Thu, 15 Mar 2018 12:54:45 +0000
Subject: [PATCH 2/2] Fix sprintf template, need this under CI

---
 lib/PCAP/Bwa.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/PCAP/Bwa.pm b/lib/PCAP/Bwa.pm
index 2157dd2..c852655 100644
--- a/lib/PCAP/Bwa.pm
+++ b/lib/PCAP/Bwa.pm
@@ -37,7 +37,7 @@ use PCAP::Bam;
 
 const my $BWA_ALN => q{ aln%s -t %s -f %s_%s.sai %s %s.%s};
 const my $BAMFASTQ => q{%s view -F 2816 -T %s -u %s| %s exclude=QCFAIL,SECONDARY,SUPPLEMENTARY tryoq=1 gz=1 level=1 outputperreadgroup=1 outputperreadgroupsuffixF=_i.fq outputperreadgroupsuffixF2=_i.fq T=%s outputdir=%s split=%s};
-const my $CRAMFASTQ => q{%s reference=%s inputformat=cram exclude=QCFAIL,SECONDARY,SUPPLEMENTARY tryoq=1 gz=1 level=1 outputperreadgroup=1 outputperreadgroupsuffixF=_i.fq outputperreadgroupsuffixF2=_i.fq T=%s outputdir=%s split=%s filename=%};
+const my $CRAMFASTQ => q{%s reference=%s inputformat=cram exclude=QCFAIL,SECONDARY,SUPPLEMENTARY tryoq=1 gz=1 level=1 outputperreadgroup=1 outputperreadgroupsuffixF=_i.fq outputperreadgroupsuffixF2=_i.fq T=%s outputdir=%s split=%s filename=%s};
 const my $BWA_MEM => q{ mem %s %s -R %s -t %s %s};
 const my $ALN_TO_SORTED => q{ sampe -P -a 1000 -r '%s' %s %s_1.sai %s_2.sai %s.%s %s.%s | %s fixmate=1 inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam};
 const my $BAMSORT => q{ fixmate=1 inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam outputthreads=%s calmdnm=1 calmdnmrecompindetonly=1 calmdnmreference=%s};