X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=samValidator.cpp;h=5586c8c3dbc1b6d46d8cd73b331fac976766296a;hp=06e91d454707c0298b47212e8fc32210bf0b74e8;hb=83ce658a4b9c5f04c081316314b66b94ad5ffbde;hpb=fb2aa1ca9d00710943155ef3abbbdd87df116e4a

diff --git a/samValidator.cpp b/samValidator.cpp
index 06e91d4..5586c8c 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;
@@ -35,7 +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!");
@@ -45,12 +46,12 @@ 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;
 
-	printf(".");
+	printf("."); fflush(stdout);
 	do {
 		if (samread(in, b) < 0) break;
 		assert(b->core.l_qseq > 0);
@@ -60,15 +61,20 @@ int main(int argc, char* argv[]) {
 		// if this is a paired-end read
 		ispaired = b->core.flag & 0x0001;
 		if (ispaired) {
+
 			isValid = (samread(in, b2) >= 0) && (qname == bam1_qname(b2)) && (b2->core.flag & 0x0001);
 			if (!isValid) { printf("\nOnly find one mate for paired-end read %s!\n", qname.c_str()); continue; }
 			assert(b2->core.l_qseq > 0);
+			isValid = !((b->core.flag & 0x0040) && (b->core.flag & 0x0080)) && !((b2->core.flag & 0x0040) & (b2->core.flag & 0x0080));
+			if (!isValid) { printf("\nRead %s has more than 2 segments (e.g. tripled or more ended reads)!\n", qname.c_str()); continue; }
 			isValid = !(((b->core.flag & 0x0040) && (b2->core.flag & 0x0040)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0080)));
 			if (!isValid) { printf("\nThe two mates of paired-end read %s are not adjacent!\n", qname.c_str()); continue; }
+
+
 			// 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);
@@ -92,7 +98,7 @@ int main(int argc, char* argv[]) {
 		}
 
 		++cnt;
-		if (cnt % 1000000 == 0) printf(".");
+		if (cnt % 1000000 == 0) { printf("."); fflush(stdout); }
 
 	} while(isValid);