From 6cb44829e3e9c08e02f04d49c2f0d00976bdb149 Mon Sep 17 00:00:00 2001
From: Keiran Raine <keiranmraine@gmail.com>
Date: Mon, 3 Aug 2015 13:04:21 +0100
Subject: [PATCH] Final resolution to #52

---
 bin/bwa_mem.pl  |  5 ++++-
 lib/PCAP/Bwa.pm | 42 ++++++++++++++++++++++++++++--------------
 2 files changed, 32 insertions(+), 15 deletions(-)

diff --git a/bin/bwa_mem.pl b/bin/bwa_mem.pl
index c9499d3..1d1cf23 100755
--- a/bin/bwa_mem.pl
+++ b/bin/bwa_mem.pl
@@ -24,6 +24,7 @@
 use autodie qw(:all);
 use FindBin qw($Bin);
 use lib "$Bin/../lib";
+use Cwd qw(abs_path);
 
 use File::Path qw(remove_tree make_path);
 use Getopt::Long;
@@ -130,7 +131,9 @@ sub setup {
   make_path($logs) unless(-d $logs);
 
   $opts{'tmp'} = $tmpdir;
-  $opts{'raw_files'} = \@ARGV;
+  for(@ARGV) {
+    push @{$opts{'raw_files'}}, abs_path($_);
+  }
 
   my $max_split = PCAP::Bwa::mem_prepare(\%opts);
 
diff --git a/lib/PCAP/Bwa.pm b/lib/PCAP/Bwa.pm
index 31c9b53..084f861 100644
--- a/lib/PCAP/Bwa.pm
+++ b/lib/PCAP/Bwa.pm
@@ -101,7 +101,7 @@ sub mem_mapmax {
     opendir(my $dh, $folder);
     while(my $file = readdir $dh) {
       next if($file =~ m/^\./);
-      next if($file =~ m/^2\.[[:digit]]+/); # captured by 1.*
+      next if($file =~ m/^pairedfq2\.[[:digit:]]+/); # captured by 1.*
       push @files, File::Spec->catfile($folder, $file);
     }
     closedir($dh);
@@ -139,21 +139,35 @@ sub split_in {
     if($input->fastq) {
       # paired fq input
       if($input->paired_fq) {
-        push @commands,  sprintf 'split -a 3 -d -l %s %s %s.'
-                                , $fragment_size * $MILLION * $PAIRED_FQ_LINE_MULT
-                                , $input->in.'_1.'.$input->fastq
-                                , File::Spec->catfile($split_folder, '1');
-        push @commands,  sprintf 'split -a 3 -d -l %s %s %s.'
-                                , $fragment_size * $MILLION * $PAIRED_FQ_LINE_MULT
-                                , $input->in.'_2.'.$input->fastq
-                                , File::Spec->catfile($split_folder, '2');
+        my $fq1 = $input->in.'_1.'.$input->fastq;
+        my $fq2 = $input->in.'_2.'.$input->fastq;
+        if($input->fastq =~ m/[.]gz$/) {
+          symlink $fq1, File::Spec->catfile($split_folder, 'pairedfq1.0.'.$input->fastq);
+          symlink $fq2, File::Spec->catfile($split_folder, 'pairedfq2.0.'.$input->fastq);
+        }
+        else {
+          push @commands,  sprintf 'split -a 3 -d -l %s %s %s.'
+                                  , $fragment_size * $MILLION * $PAIRED_FQ_LINE_MULT
+                                  , $fq1
+                                  , File::Spec->catfile($split_folder, 'pairedfq1');
+          push @commands,  sprintf 'split -a 3 -d -l %s %s %s.'
+                                  , $fragment_size * $MILLION * $PAIRED_FQ_LINE_MULT
+                                  , $fq2
+                                  , File::Spec->catfile($split_folder, 'pairedfq2');
+        }
       }
       # interleaved FQ
       else {
-        push @commands,  sprintf 'split -a 3 -d -l %s %s %s.'
-                                , $fragment_size * $MILLION * $INTERLEAVED_FQ_LINE_MULT
-                                , $input->in.'.'.$input->fastq
-                                , File::Spec->catfile($split_folder, 'i');
+        my $fq_i = $input->in.'.'.$input->fastq;
+        if($input->fastq =~ m/[.]gz$/) {
+          symlink $fq_i, File::Spec->catfile($split_folder, 'i.'.$input->fastq);
+        }
+        else {
+          push @commands,  sprintf 'split -a 3 -d -l %s %s %s.'
+                                  , $fragment_size * $MILLION * $INTERLEAVED_FQ_LINE_MULT
+                                  , $fq_i
+                                  , File::Spec->catfile($split_folder, 'i');
+        }
       }
     }
     # if bam input
@@ -227,7 +241,7 @@ sub bwa_mem {
     # uncoverable branch false
     if($input->paired_fq) {
       my $split2 = $split;
-      $split2 =~ s/1(\.[[:digit:]]+)$/2$1/;
+      $split2 =~ s/pairedfq1(\.[[:digit:]]+)/pairedfq2$1/;
       $bwa .= ' '.$split;
       $bwa .= ' '.$split2;
     }