X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=samValidator.cpp;h=5586c8c3dbc1b6d46d8cd73b331fac976766296a;hp=5b02ba4c46f41f20884915d7f117c2a3213f49b0;hb=83ce658a4b9c5f04c081316314b66b94ad5ffbde;hpb=9eef8b58056b7cdaad1b4bdb2b2904d9fc0ff430

diff --git a/samValidator.cpp b/samValidator.cpp
index 5b02ba4..5586c8c 100644
--- a/samValidator.cpp
+++ b/samValidator.cpp
@@ -36,7 +36,7 @@ int main(int argc, char* argv[]) {
 	size_t len = suffix.length();
 	for (size_t i = 0; i < len; i++) suffix[i] = tolower(suffix[i]);
 
-	general_assert(suffix == "sam" || suffix == "bam", "Cannot recognize input file's file type! The file suffix is neither sam or bam.");
+	general_assert(suffix == "sam" || suffix == "bam", "Cannot recognize input file's file type! The file suffix is neither sam nor bam.");
 
 	in = (suffix == "sam" ? samopen(argv[1], "r", NULL) : samopen(argv[1], "rb", NULL));
 	general_assert(in != 0, "Cannot open input file!");
@@ -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);