#include "sam/sam.h"
#include "utils.h"
-
-#include "Transcript.h"
-#include "Transcripts.h"
+#include "my_assert.h"
#include "SingleRead.h"
#include "SingleReadQ.h"
#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();
/**
bam_header_t *header;
bam1_t *b, *b2;
+ Transcripts& transcripts;
//tag used by aligner
static char rtTag[STRLEN];
}
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*);
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() {
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);
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);
}
}
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);
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);
}
}
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);
}
//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);
}
}
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);
}
//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);
}
}
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;
}
projects / rsem.git / blobdiff