Empty bam files except header now produce RG information and a line o…

…f zeroes
cancerit · Jul 11, 2017 · c4b3652 · c4b3652
1 parent 8e185e4
commit c4b3652
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,6 @@
+### 4.0.5
+* bam_stats now outputs a line of zeroes for bam files with zero reads
+
 ### 3.5.0
 * Adds RNA downloads to PanCancer download tool `gnos_pull.pl`
 * Hardening of external process handling in `PCAP::Threaded`

diff --git a/c/bam_stats_output.c b/c/bam_stats_output.c
@@ -42,7 +42,7 @@ int bam_stats_output_print_results(rg_info_t **grps,int grps_size,stats_rd_t***
   //Iterate through each RG
   int i=0;
   for(i=0;i<grps_size;i++){
-    if(grp_stats[i][0]->count==0 && grp_stats[i][1]->count==0) continue; // Skip empty read groups stats
+
     uint64_t unmapped_r1 = grp_stats[i][0]->umap;
     uint64_t unmapped_r2 = grp_stats[i][1]->umap;
     uint64_t unmapped =  grp_stats[i][0]->umap + grp_stats[i][1]->umap;

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 = '4.0.4';
+our $VERSION = '4.0.5';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>