Modified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved...

diff --git a/BamConverter.h b/BamConverter.h
index 4ea7d3e673e3942e4de7a678acb5be15faf03c11..d36f3d10c4d4e78ab4351f7482477fc77d318e07 100644 (file)
--- a/BamConverter.h
+++ b/BamConverter.h
@@ -227,7 +227,8 @@ inline void BamConverter::writeCollapsedLines() {
                                memcpy(bam_aux_get(tmp_b, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));
                                tmp_b->core.qual = getMAPQ(prb);
                        }
-                       else tmp_b->core.qual = getMAPQ(1.0);
+                       // otherwise, just use the MAPQ score of the orignal alignment
+
                        samwrite(out, tmp_b);
                        if (isPaired) {
                                if (p != NULL) memcpy(bam_aux_get(tmp_b2, "ZW") + 1, (uint8_t*)&(prb), bam_aux_type2size('f'));

diff --git a/rsem_perl_utils.pm b/rsem_perl_utils.pm
index f3edfe4713353e8bbfec0698a6e2510e80d25a42..b2a040f53be5ed4b53d4e278008697167dfb7dfe 100644 (file)
--- a/rsem_perl_utils.pm
+++ b/rsem_perl_utils.pm
@@ -90,7 +90,7 @@ sub showVersionInfo {
     my $line = <INPUT>;
     chomp($line);
     close(INPUT);
-    print "$line\n";
+    print "Current version is $line\n";
     exit(0);
 }