X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=SamParser.h;h=e91f9c379539fc7ada0f8682bcfc7c957489d67f;hp=a36af3a0d11a7133b27c5ee4fe83ae7996b9f631;hb=636b82d9f60ebcbec7ef1b73ba23bbbacfd8b36a;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387

diff --git a/SamParser.h b/SamParser.h
index a36af3a..e91f9c3 100644
--- a/SamParser.h
+++ b/SamParser.h
@@ -1,4 +1,4 @@
-/* ReadType here means if the read is unalignable, alignable or aligned too much. It is NOT single read or paired-end read */
+/* ReadType here means if the read is unalignable, alignable or aligned too much. It is NOT siheaderngle read or paired-end read */
 #ifndef SAMPARSER_H_
 #define SAMPARSER_H_
 
@@ -10,7 +10,10 @@
 
 #include "sam/bam.h"
 #include "sam/sam.h"
+
 #include "utils.h"
+#include "my_assert.h"
+
 #include "SingleRead.h"
 #include "SingleReadQ.h"
 #include "PairedEndRead.h"
@@ -18,9 +21,11 @@
 #include "SingleHit.h"
 #include "PairedEndHit.h"
 
+#include "Transcripts.h"
+
 class SamParser {
 public:
-	SamParser(char, const char*, const char* = 0);
+	SamParser(char, const char*, Transcripts&, const char* = 0);
 	~SamParser();
 
 	/**
@@ -46,6 +51,8 @@ private:
 	bam_header_t *header;
 	bam1_t *b, *b2;
 
+	Transcripts& transcripts;
+
 	//tag used by aligner
 	static char rtTag[STRLEN];
 
@@ -64,24 +71,32 @@ private:
 	//0 ~ N0 1 ~ N1 2 ~ N2
 	int getReadType(const bam1_t*);
 	int getReadType(const bam1_t*, const bam1_t*); // for paired-end reads
+
+	bool check(bam1_t *b) {
+		return (b->core.n_cigar == 1) && ((*bam1_cigar(b) & BAM_CIGAR_MASK) == BAM_CMATCH) && (b->core.l_qseq == (int32_t)(*bam1_cigar(b) >> BAM_CIGAR_SHIFT));
+	}
 };
 
 char SamParser::rtTag[STRLEN] = ""; // default : no tag, thus no Type 2 reads
 
 // aux, if not 0, points to the file name of fn_list
-SamParser::SamParser(char inpType, const char* inpF, const char* aux) {
+SamParser::SamParser(char inpType, const char* inpF, Transcripts& transcripts, const char* aux)
+	: transcripts(transcripts)
+{
 	switch(inpType) {
 	case 'b': sam_in = samopen(inpF, "rb", aux); break;
 	case 's': sam_in = samopen(inpF, "r", aux); break;
 	default: assert(false);
 	}
 
-	if (sam_in == 0) { fprintf(stderr, "Cannot open %s! It may not exist.\n", inpF); exit(-1); }
-    header = sam_in->header;
-    if (header == 0) { fprintf(stderr, "Fail to parse sam header!\n"); exit(-1); }
+	general_assert(sam_in != 0, "Cannot open " + cstrtos(inpF) + "! It may not exist.");
+	header = sam_in->header;
+	general_assert(header != 0, "Fail to parse sam header!");
 
-    b = bam_init1();
-    b2 = bam_init1();
+	transcripts.buildMappings(header->n_targets, header->target_name);
+
+	b = bam_init1();
+	b2 = bam_init1();
 }
 
 SamParser::~SamParser() {
@@ -97,8 +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);
@@ -110,11 +124,13 @@ int SamParser::parseNext(SingleRead& read, SingleHit& hit) {
 	else val = 5;
 
 	if (readType == 1) {
+		if (!check(b)) { fprintf(stderr, "RSEM does not support gapped alignments, sorry!\n"); exit(-1); }
+
 		if (getDir(b) > 0) {
-			hit = SingleHit(b->core.tid + 1, b->core.pos);
+			hit = SingleHit(transcripts.getInternalSid(b->core.tid + 1), b->core.pos);
 		}
 		else {
-			hit = SingleHit(-(b->core.tid + 1), header->target_len[b->core.tid] - b->core.pos - b->core.l_qseq);
+			hit = SingleHit(-transcripts.getInternalSid(b->core.tid + 1), header->target_len[b->core.tid] - b->core.pos - b->core.l_qseq);
 		}
 	}
 
@@ -126,8 +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);
@@ -139,11 +154,13 @@ int SamParser::parseNext(SingleReadQ& read, SingleHit& hit) {
 	else val = 5;
 
 	if (readType == 1) {
+		if (!check(b)) { fprintf(stderr, "RSEM does not support gapped alignments, sorry!\n"); exit(-1); }
+
 		if (getDir(b) > 0) {
-			hit = SingleHit(b->core.tid + 1, b->core.pos);
+			hit = SingleHit(transcripts.getInternalSid(b->core.tid + 1), b->core.pos);
 		}
 		else {
-			hit = SingleHit(-(b->core.tid + 1), header->target_len[b->core.tid] - b->core.pos - b->core.l_qseq);
+			hit = SingleHit(-transcripts.getInternalSid(b->core.tid + 1), header->target_len[b->core.tid] - b->core.pos - b->core.l_qseq);
 		}
 	}
 
@@ -156,21 +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);
@@ -184,16 +202,18 @@ int SamParser::parseNext(PairedEndRead& read, PairedEndHit& hit) {
 	else val = 5;
 
 	if (readType == 1) {
+		if (!check(mp1) || !check(mp2)) { fprintf(stderr, "RSEM does not support gapped alignments, sorry!\n"); exit(-1); }
+
 		if (mp1->core.tid != mp2->core.tid) {
 			fprintf(stderr, "The two reads do not come from the same pair!");
 			exit(-1);
 		}
 		//assert(mp1->core.tid == mp2->core.tid);
 		if (getDir(mp1) > 0) {
-			hit = PairedEndHit(mp1->core.tid + 1, mp1->core.pos, mp2->core.pos + mp2->core.l_qseq - mp1->core.pos);
+			hit = PairedEndHit(transcripts.getInternalSid(mp1->core.tid + 1), mp1->core.pos, mp2->core.pos + mp2->core.l_qseq - mp1->core.pos);
 		}
 		else {
-			hit = PairedEndHit(-(mp1->core.tid + 1), header->target_len[mp1->core.tid] - mp1->core.pos - mp1->core.l_qseq, mp1->core.pos + mp1->core.l_qseq - mp2->core.pos);
+			hit = PairedEndHit(-transcripts.getInternalSid(mp1->core.tid + 1), header->target_len[mp1->core.tid] - mp1->core.pos - mp1->core.l_qseq, mp1->core.pos + mp1->core.l_qseq - mp2->core.pos);
 		}
 	}
 
@@ -205,21 +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);
@@ -233,16 +254,18 @@ int SamParser::parseNext(PairedEndReadQ& read, PairedEndHit& hit) {
 	else val = 5;
 
 	if (readType == 1) {
+		if (!check(mp1) || !check(mp2)) { fprintf(stderr, "RSEM does not support gapped alignments, sorry!\n"); exit(-1); }
+
 		if (mp1->core.tid != mp2->core.tid) {
 			fprintf(stderr, "The two reads do not come from the same pair!");
 			exit(-1);
 		}
 		//assert(mp1->core.tid == mp2->core.tid);
 		if (getDir(mp1) > 0) {
-			hit = PairedEndHit(mp1->core.tid + 1, mp1->core.pos, mp2->core.pos + mp2->core.l_qseq - mp1->core.pos);
+			hit = PairedEndHit(transcripts.getInternalSid(mp1->core.tid + 1), mp1->core.pos, mp2->core.pos + mp2->core.l_qseq - mp1->core.pos);
 		}
 		else {
-			hit = PairedEndHit(-(mp1->core.tid + 1), header->target_len[mp1->core.tid] - mp1->core.pos - mp1->core.l_qseq, mp1->core.pos + mp1->core.l_qseq - mp2->core.pos);
+			hit = PairedEndHit(-transcripts.getInternalSid(mp1->core.tid + 1), header->target_len[mp1->core.tid] - mp1->core.pos - mp1->core.l_qseq, mp1->core.pos + mp1->core.l_qseq - mp2->core.pos);
 		}
 	}
 
@@ -318,10 +341,17 @@ inline int SamParser::getReadType(const bam1_t* b) {
 	return (bam_aux2i(p) > 0 ? 2 : 0);
 }
 
-
 //For paired-end reads, do not print out type 2 reads
 inline int SamParser::getReadType(const bam1_t* b, const bam1_t* b2) {
-	if ((b->core.flag & 0x0002) && (b2->core.flag & 0x0002)) return 1;
+	if (!(b->core.flag & 0x0004) && !(b2->core.flag & 0x0004)) return 1;
+
+	if (!strcmp(rtTag, "")) return 0;
+
+	uint8_t *p = bam_aux_get(b, rtTag);
+	if (p != NULL && bam_aux2i(p) > 0) return 2;
+
+	p = bam_aux_get(b2, rtTag);
+	if (p != NULL && bam_aux2i(p) > 0) return 2;
 
 	return 0;
 }