X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=scanForPairedEndReads.cpp;h=3669f5faad46972a6b2949a2226a6a159f284b67;hp=751fa558833aabce8bac0ae4d02013aae0ac1685;hb=d13cdd443afbefff6f7c8c0be818e1edcbc9cb8d;hpb=9eef8b58056b7cdaad1b4bdb2b2904d9fc0ff430

diff --git a/scanForPairedEndReads.cpp b/scanForPairedEndReads.cpp
index 751fa55..3669f5f 100644
--- a/scanForPairedEndReads.cpp
+++ b/scanForPairedEndReads.cpp
@@ -29,15 +29,23 @@ inline void add_to_appropriate_arr(bam1_t *b) {
 	else arr_partial_unknown.push_back(bam_dup1(b));
 }
 
+char get_pattern_code(uint32_t flag) {
+  if (flag & 0x0040) return (flag & 0x0010 ? 1 : 0);
+  else return (flag & 0x0010 ? 0 : 1);
+}
+
 bool less_than(bam1_t *a, bam1_t *b) {
 	int32_t ap1 = min(a->core.pos, a->core.mpos);
 	int32_t ap2 = max(a->core.pos, a->core.mpos);
 	int32_t bp1 = min(b->core.pos, b->core.mpos);
 	int32_t bp2 = max(b->core.pos, b->core.mpos);
+	char apat = get_pattern_code(a->core.flag); // apt: a's pattern of strand and mate information
+	char bpat = get_pattern_code(b->core.flag);
 
 	if (a->core.tid != b->core.tid) return a->core.tid < b->core.tid;
 	if (ap1 != bp1) return ap1 < bp1;
-	return ap2 < bp2;
+	if (ap2 != bp2) return ap2 < bp2;
+	return apat < bpat;
 }
 
 int main(int argc, char* argv[]) {
@@ -67,12 +75,12 @@ int main(int argc, char* argv[]) {
 		if (isPaired) {
 			add_to_appropriate_arr(b);
 			while ((go_on = (samread(in, b) >= 0)) && (qname == bam1_qname(b))) {
-				general_assert(b->core.flag & 0x0001, "Read " + qname + " is detected as both single-end and paired-end read!", true);
+				general_assert_1(b->core.flag & 0x0001, "Read " + qname + " is detected as both single-end and paired-end read!");
 				add_to_appropriate_arr(b);
 			}
 
-			general_assert(arr_both.size() % 2 == 0, "Number of first and second mates in read " + qname + "'s full alignments (both mates are aligned) are not matched!", true);
-			general_assert((arr_partial_1.size() + arr_partial_2.size() + arr_partial_unknown.size()) % 2 == 0, "Number of first and second mates in read " + qname + "'s partial alignments (at most one mate is aligned) are not matched!", true);
+			general_assert_1(arr_both.size() % 2 == 0, "Number of first and second mates in read " + qname + "'s full alignments (both mates are aligned) are not matched!");
+			general_assert_1((arr_partial_1.size() + arr_partial_2.size() + arr_partial_unknown.size()) % 2 == 0, "Number of first and second mates in read " + qname + "'s partial alignments (at most one mate is aligned) are not matched!");
 
 			if (!arr_both.empty()) {
 				sort(arr_both.begin(), arr_both.end(), less_than);