X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=samValidator.cpp;h=6e602107090f1d795341f9c08ee3b7d27689ae22;hp=e1a2cc8c8aefee07e6c747f5391e5b369063d4ec;hb=7777bfc71742d4e239d1297d2e3de058895f4ce1;hpb=d5639baddcd4bdf09dd31237e914afb987954472

diff --git a/samValidator.cpp b/samValidator.cpp
index e1a2cc8..6e60210 100644
--- a/samValidator.cpp
+++ b/samValidator.cpp
@@ -9,6 +9,7 @@
 #include "sam/bam.h"
 #include "sam/sam.h"
 
+#include "utils.h"
 #include "my_assert.h"
 
 using namespace std;
@@ -45,7 +46,7 @@ int main(int argc, char* argv[]) {
 
 	isValid = true;
 
-	long cnt = 0;
+	HIT_INT_TYPE cnt = 0;
 	string cqname(""), qname;
 	uint64_t creadlen = 0, readlen;
 	bool cispaired = false, ispaired;
@@ -73,7 +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);