From: Bo Li <bli@cs.wisc.edu>
Date: Fri, 27 Jul 2012 16:46:25 +0000 (-0500)
Subject: Added a user-friendly error message for rsem-sam-validator
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=7777bfc71742d4e239d1297d2e3de058895f4ce1;hp=7f503f1b9e22d7e1b44472add2263f263675b7c7

Added a user-friendly error message for rsem-sam-validator
---

diff --git a/samValidator.cpp b/samValidator.cpp
index 5b02ba4..6e60210 100644
--- a/samValidator.cpp
+++ b/samValidator.cpp
@@ -74,7 +74,7 @@ int main(int argc, char* argv[]) {
 			// both mates are mapped
 			if (!(b->core.flag & 0x0004) && !(b2->core.flag & 0x0004)) {
 				isValid = (b->core.tid == b2->core.tid) && (b->core.pos == b2->core.mpos) && (b2->core.pos == b->core.mpos);
-				if (!isValid) { printf("\nOne of paired-end read %s's alignment does not have two mates adjacent to each other!\n", qname.c_str()); continue; }
+				if (!isValid) { printf("\nOne of paired-end read %s's alignment does not have two mates adjacent to each other! If you're running covert-sam-for-rsem now, this might mean the read contains duplicate alignments.\n", qname.c_str()); continue; }
 			}
 
 			readlen = ((b->core.flag & 0x0040) ? (uint64_t(b->core.l_qseq) << 32) + b2->core.l_qseq : (uint64_t(b2->core.l_qseq) << 32) + b->core.l_qseq);