From 7777bfc71742d4e239d1297d2e3de058895f4ce1 Mon Sep 17 00:00:00 2001 From: Bo Li Date: Fri, 27 Jul 2012 11:46:25 -0500 Subject: [PATCH] Added a user-friendly error message for rsem-sam-validator --- samValidator.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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); -- 2.39.2