X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=SamParser.h;h=4747ef4281af593f714450d68ccfc65090662891;hp=335984e7394f2645ef4ee178032c57799c69d312;hb=refs%2Fheads%2Fmaster;hpb=58f823f5be6dfbe00896fc44ac3aac5e881e9c5c

diff --git a/SamParser.h b/SamParser.h
index 335984e..4747ef4 100644
--- a/SamParser.h
+++ b/SamParser.h
@@ -12,9 +12,7 @@
 #include "sam/sam.h"
 
 #include "utils.h"
-
-#include "Transcript.h"
-#include "Transcripts.h"
+#include "my_assert.h"
 
 #include "SingleRead.h"
 #include "SingleReadQ.h"
@@ -23,9 +21,11 @@
 #include "SingleHit.h"
 #include "PairedEndHit.h"
 
+#include "Transcripts.h"
+
 class SamParser {
 public:
-	SamParser(char, const char*, Transcripts&, const char* = 0);
+	SamParser(char, const char*, const char*, Transcripts&, const char*);
 	~SamParser();
 
 	/**
@@ -51,6 +51,7 @@ private:
 	bam_header_t *header;
 	bam1_t *b, *b2;
 
+	Transcripts& transcripts;
 
 	//tag used by aligner
 	static char rtTag[STRLEN];
@@ -61,7 +62,7 @@ private:
 	}
 
 	std::string getName(const bam1_t* b) {
-		return std::string((char*)bam1_qname(b));
+		return std::string(bam1_qname(b));
 	}
 
 	std::string getReadSeq(const bam1_t*);
@@ -79,33 +80,23 @@ private:
 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, Transcripts& transcripts, const char* aux) {
+SamParser::SamParser(char inpType, const char* inpF, const char* aux, Transcripts& transcripts, const char* imdName)
+	: 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); }
-
-    // Check if the reference used for aligner is the transcript set RSEM generated
-    if (transcripts.getM() != header->n_targets) {
-    	fprintf(stderr, "Number of transcripts does not match! Please align reads against the transcript set and use RSEM generated reference for your aligner!\n");
-    	exit(-1);
-    }
-    for (int i = 0; i < header->n_targets; i++) {
-    	const Transcript& transcript = transcripts.getTranscriptAt(i + 1);
-    	// If update int to long, chance the (int) conversion
-    	if (transcript.getTranscriptID().compare(header->target_name[i]) != 0 || transcript.getLength() != (int)header->target_len[i]) {
-    		fprintf(stderr, "Transcript information does not match! Please align reads against the transcript set and use RSEM generated reference for your aligner!\n");
-    		exit(-1);
-    	}
-    }
-
-    b = bam_init1();
-    b2 = bam_init1();
+	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!");
+
+	transcripts.buildMappings(header->n_targets, header->target_name, imdName);
+
+	b = bam_init1();
+	b2 = bam_init1();
 }
 
 SamParser::~SamParser() {
@@ -121,8 +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);
@@ -137,10 +127,10 @@ int SamParser::parseNext(SingleRead& read, SingleHit& hit) {
 		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);
 		}
 	}
 
@@ -152,8 +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);
@@ -168,10 +157,10 @@ int SamParser::parseNext(SingleReadQ& read, SingleHit& hit) {
 		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);
 		}
 	}
 
@@ -184,21 +173,24 @@ 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?
+
+	general_assert(!strcmp(bam1_qname(mp1), bam1_qname(mp2)), "Detected a read pair whose two mates have different names: " + getName(mp1) + " , " + getName(mp2) + " !");
 
 	int readType = getReadType(mp1, mp2);
 	std::string name = getName(mp1);
@@ -220,10 +212,10 @@ int SamParser::parseNext(PairedEndRead& read, PairedEndHit& hit) {
 		}
 		//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);
 		}
 	}
 
@@ -235,21 +227,24 @@ 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;
+
+	general_assert(!strcmp(bam1_qname(mp1), bam1_qname(mp2)), "Detected a read pair whose two mates have different names: " + getName(mp1) + " , " + getName(mp2) + " !");
 
 	int readType = getReadType(mp1, mp2);
 	std::string name = getName(mp1);
@@ -271,10 +266,10 @@ int SamParser::parseNext(PairedEndReadQ& read, PairedEndHit& hit) {
 		}
 		//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);
 		}
 	}
 
@@ -350,10 +345,17 @@ 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;
 }