X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=BamConverter.h;h=037be8953891a38c4ad94ba2d888e114af601351;hp=d36f3d10c4d4e78ab4351f7482477fc77d318e07;hb=2d71eb92104693ca9baa5a2e1c23eeca776d8fd3;hpb=142c0168622638bb25f09796c3598fab28a1f94c

diff --git a/BamConverter.h b/BamConverter.h
index d36f3d1..037be89 100644
--- a/BamConverter.h
+++ b/BamConverter.h
@@ -119,14 +119,13 @@ void BamConverter::process() {
 		// at least one segment is not properly mapped
 		bool notgood = (b->core.flag & 0x0004) || (isPaired && (b2->core.flag & 0x0004));
 		
-
-		if (isPaired && notgood) assert((b->core.flag & 0x0004) && (b2->core.flag & 0x0004));
-
+		if (isPaired && notgood) general_assert((b->core.flag & 0x0004) && (b2->core.flag & 0x0004), cstrtos(bam1_qname(b)) + "'s two mates are not all marked as unalignable!");
 
 		if (!notgood) {
 			// for collapsing
 			if (isPaired) {
 				assert(b->core.tid == b2->core.tid);
+				general_assert(b->core.tid == b2->core.tid, cstrtos(bam1_qname(b)) + "'s two mates are aligned to two different transcripts!");
 				if ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)) {
 					bam1_t *tmp = b; b = b2; b2 = tmp;
 				}