X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=SamParser.h;h=513536f2a2107e181a0393946a00e9fa77c35416;hp=c5a503554b8c9cf4716b722d47da5f8c5db8540c;hb=683863b75f8d8bef2461039a6911b0e9619cc113;hpb=237bbdf363c9e42ee24e2fd63106dccf20d9bf2f

diff --git a/SamParser.h b/SamParser.h
index c5a5035..513536f 100644
--- a/SamParser.h
+++ b/SamParser.h
@@ -112,8 +112,7 @@ int SamParser::parseNext(SingleRead& read, SingleHit& hit) {
 	bool canR = (samread(sam_in, b) >= 0);
 	if (!canR) return -1;
 
-	if (b->core.flag & 0x0001) { fprintf(stderr, "Find a paired end read in the file!\n"); exit(-1); }
-	//(b->core.flag & 0x0100) &&  && !(b->core.flag & 0x0004)
+	general_assert(!(b->core.flag & 0x0001), "Find a paired end read in the file!");
 
 	int readType = getReadType(b);
 	std::string name = getName(b);
@@ -143,8 +142,7 @@ int SamParser::parseNext(SingleReadQ& read, SingleHit& hit) {
 	bool canR = (samread(sam_in, b) >= 0);
 	if (!canR) return -1;
 
-	if (b->core.flag & 0x0001) { fprintf(stderr, "Find a paired end read in the file!\n"); exit(-1); }
-	//assert(!(b->core.flag & 0x0001)); //(b->core.flag & 0x0100) &&  && !(b->core.flag & 0x0004)
+	general_assert(!(b->core.flag & 0x0001), "Find a paired end read in the file!");
 
 	int readType = getReadType(b);
 	std::string name = getName(b);
@@ -175,21 +173,22 @@ int SamParser::parseNext(PairedEndRead& read, PairedEndHit& hit) {
 	bool canR = ((samread(sam_in, b) >= 0) && (samread(sam_in, b2) >= 0));
 	if (!canR) return -1;
 
-	if (!((b->core.flag & 0x0001) && (b2->core.flag & 0x0001))) {
-		fprintf(stderr, "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)\n");
-		exit(-1);
-	}
-	//assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
+	general_assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001), \
+			"One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)");
 
 	bam1_t *mp1 = NULL, *mp2 = NULL;
 
-	if ((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) {
+	// If lose mate info, discard. is it necessary?
+	if (!((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) && !((b->core.flag & 0x0080) && (b2->core.flag & 0x0040))) return 4;
+	// If only one mate is mapped, discard
+	if (((b->core.flag & 0x0004) && !(b2->core.flag & 0x0004)) || (!(b->core.flag & 0x0004) && (b2->core.flag & 0x0004))) return 4;
+
+	if (b->core.flag & 0x0040) {
 		mp1 = b; mp2 = b2;
 	}
-	else if ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)) {
+	else  {
 		mp1 = b2; mp2 = b;
 	}
-	else return 4; // If lose mate info, discard. is it necessary?
 
 	int readType = getReadType(mp1, mp2);
 	std::string name = getName(mp1);
@@ -226,21 +225,22 @@ int SamParser::parseNext(PairedEndReadQ& read, PairedEndHit& hit) {
 	bool canR = ((samread(sam_in, b) >= 0) && (samread(sam_in, b2) >= 0));
 	if (!canR) return -1;
 
-	if (!((b->core.flag & 0x0001) && (b2->core.flag & 0x0001))) {
-		fprintf(stderr, "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)\n");
-		exit(-1);
-	}
-	//assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
+	general_assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001), \
+			"One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)");
 
 	bam1_t *mp1 = NULL, *mp2 = NULL;
 
-	if ((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) {
+	// If lose mate info, discard. is it necessary?
+	if (!((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) && !((b->core.flag & 0x0080) && (b2->core.flag & 0x0040))) return 4;
+	// If only one mate is mapped, discard
+	if (((b->core.flag & 0x0004) && !(b2->core.flag & 0x0004)) || (!(b->core.flag & 0x0004) && (b2->core.flag & 0x0004))) return 4;
+
+	if (b->core.flag & 0x0040) {
 		mp1 = b; mp2 = b2;
 	}
-	else if ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)) {
+	else  {
 		mp1 = b2; mp2 = b;
 	}
-	else return 4;
 
 	int readType = getReadType(mp1, mp2);
 	std::string name = getName(mp1);