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// DECLARATIONS: {{{
#include<cmath>
#include<set>
using namespace std;
#include "ArgumentParser.h"
#include "misc.h"
#include "MyTimer.h"
#include "ReadDistribution.h"
#include "TranscriptExpression.h"
#include "TranscriptInfo.h"
#include "TranscriptSequence.h"
#include "common.h"
//}}}
//#define DEBUG_AT(x) message(x)
#define DEBUG_AT(x)
namespace ns_parseAlignment {
class TagAlignment{//{{{
protected:
int_least32_t trId;
// bool strand; // true = forward; false = reverse
double prob,lowProb;
public:
TagAlignment(long t=0,double p = 0,double lp = 0){
trId=(int_least32_t)t;
// strand=s;
prob=p;
lowProb=lp;
}
long getTrId()const {return trId;}
double getProb()const {return prob;}
double getLowProb()const {return lowProb;}
void setProb(double p){prob=p;}
}; //}}}
// Check if next fragment is different.
bool nextFragDiffers(const ns_rD::fragmentP curF, const ns_rD::fragmentP nextF, bool mateNamesDiffer);
// String comparison allowing last cmpEPS bases different as long as length
// is the same.
long readNameCmp(const char *str1, const char *str2);
// Read Fragment from SAM file.
// Copies data from 'next' fragment into 'cur' fragment and reads new fragment information into 'next'.
// Fragment is either both paired-ends or just single read.
bool readNextFragment(samfile_t* samData, ns_rD::fragmentP &cur, ns_rD::fragmentP &next);
// Determine input format base either on --format flag or on the file extension.
// Sets format to bam/sam and returns true, or returns false if format is unknown.
bool setInputFormat(const ArgumentParser &args, string *format);
bool openSamFile(const string &name, const string &inFormat, samfile_t **samFile);
bool initializeInfoFile(const ArgumentParser &args, samfile_t *samFile, TranscriptInfo **trInfo, long *M);
} // namespace ns_parseAlignment
extern "C" int parseAlignment(int *argc,char* argv[]){
string programDescription =
"Pre-computes probabilities of (observed) reads' alignments.\n\
[alignment file] should be in either SAM or BAM format.\n";
TranscriptInfo *trInfo=NULL;
TranscriptSequence *trSeq=NULL;
TranscriptExpression *trExp=NULL;
MyTimer timer;
timer.start();
timer.start(7);
long Ntotal = 0, Nmap = 0, M=0, i;
string inFormat;
samfile_t *samData=NULL;
ReadDistribution readD;
ns_rD::fragmentP curF = new ns_rD::fragmentT, nextF = new ns_rD::fragmentT, validAF = new ns_rD::fragmentT;
// This could be changed to either GNU's hash_set or C++11's unsorted_set, once it's safe.
set<string> ignoredReads;
long ignoredMaxAlignments = 0, ignoredSingletons = 0;
// Intro: {{{
// Set options {{{
ArgumentParser args(programDescription,"[alignment file]",1);
args.addOptionS("o","outFile","outFileName",1,"Name of the output file.");
args.addOptionS("f","format","format",0,"Input format: either SAM, BAM.");
args.addOptionS("t","trInfoFile","trInfoFileName",0,"File to save transcript information extracted from [BS]AM file and reference.");
//args.addOptionS("t","trInfoFile","trInfoFileName",0,"If transcript(reference sequence) information is contained within SAM file, program will write this information into <trInfoFile>, otherwise it will look for this information in <trInfoFile>.");
args.addOptionS("s","trSeqFile","trSeqFileName",1,"Transcript sequence in FASTA format --- for non-uniform read distribution estimation.");
args.addOptionS("","trSeqHeader","trSeqHeader",0,"Transcript sequence header format enables gene name extraction (standard/gencode).","standard");
args.addOptionS("e","expressionFile","expFileName",0,"Transcript relative expression estimates --- for better non-uniform read distribution estimation.");
args.addOptionL("N","readsN","readsN",0,"Total number of reads. This is not necessary if [SB]AM contains also reads with no valid alignments.");
args.addOptionS("","failed","failed",0,"File name where to save names of reads that failed to align.");
args.addOptionB("","uniform","uniform",0,"Use uniform read distribution.");
args.addOptionD("","lenMu","lenMu",0,"Set mean of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2))");
args.addOptionD("","lenSigma","lenSigma",0,"Set sigma^2 (or variance) of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2))");
args.addOptionS("","distributionFile","distributionFileName",0,"Name of file to which read-distribution should be saved.");
args.addOptionL("P","procN","procN",0,"Maximum number of threads to be used. This provides speedup mostly when using non-uniform read distribution model (i.e. no --uniform flag).",4);
args.addOptionB("V","veryVerbose","veryVerbose",0,"Very verbose output.");
args.addOptionL("","noiseMismatches","numNoiseMismatches",0,"Number of mismatches to be considered as noise.",ns_rD::LOW_PROB_MISSES);
args.addOptionL("l","limitA","maxAlignments",0,"Limit maximum number of alignments per read. (Reads with more alignments are skipped.)");
args.addOptionB("","unstranded","unstranded",0,"Paired read are not strand specific.");
args.addOptionB("","show1warning","show1warning",0,"Show first alignments that are considered wrong (TID unknown, TID mismatch, wrong strand).");
args.addOptionB("","excludeSingletons","excludeSingletons",0,"Exclude single mate alignments for paired-end reads.");
args.addOptionB("","mateNamesDiffer","mateNamesDiffer",0,"Mates from paired-end reads have different names.");
if(!args.parse(*argc,argv))return 0;
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
readD.setProcN(args.getL("procN"));
if(args.flag("show1warning"))readD.showFirstWarnings();
// }}}
if(!ns_parseAlignment::setInputFormat(args, &inFormat))return 1;
if(!ns_parseAlignment::openSamFile(args.args()[0], inFormat, &samData))return 1;
if(!ns_parseAlignment::initializeInfoFile(args, samData, &trInfo, &M))return 1;
// Read expression and initialize transcript sequence {{{
if(args.verbose)message("Initializing fasta sequence reader.\n");
// Initialize fasta sequence reader.
trSeq = new TranscriptSequence();
if(args.getLowerS("trSeqHeader") == "gencode"){
trSeq->readSequence(args.getS("trSeqFileName"), GENCODE);
}else{
trSeq->readSequence(args.getS("trSeqFileName"), STANDARD);
}
// Check numbers for transcripts match.
if(trSeq->getM() != M){
error("Main: Number of transcripts in the alignment file and the sequence file are different: %ld vs %ld\n",M,trSeq->getM());
return 1;
}
// Check that length of each transcript matches.
for(i=0;i<M;i++){
if(trInfo->L(i) != (long)(trSeq->getTr(i).size())){
error("Main: Transcript info length and sequence length of transcript %ld DO NOT MATCH! (%ld %d)\n",i,trInfo->L(i),(int)(trSeq->getTr(i).size()));
return 1;
}
}
// If there were gene names in transcript sequence, assign them to transcript info.
if(trSeq->hasGeneNames() && (trSeq->getG()>1)){
if(trInfo->getG() == 1){
// If just one gene present, then assign gene names.
if(args.verbose)message("Found gene names in sequence file, updating transcript information.\n");
trInfo->updateGeneNames(trSeq->getGeneNames());
}else{
// If there is more than one gene name already, don't fix.
if(trInfo->getG() != trSeq->getG()){
warning("Main: Different number of genes detected in transcript information and sequence file (%ld %ld).\n You might want to check your data.\n", trInfo->getG(), trSeq->getG());
}
}
}
// If format is GENCODE and transcript names were extracted, update.
if((args.getLowerS("trSeqHeader") == "gencode")&&(trSeq->hasTrNames())){
if(args.flag("veryVerbose"))message("Updating transcript names.\n");
if(!trInfo->updateTrNames(trSeq->getTrNames())){
if(args.flag("veryVerbose"))warning("Transcript names update failed.\n");
}
}
if(!args.flag("uniform")){
// Try loading expression file from previous estimation for non-uniform read model.
if(args.isSet("expFileName")){
if(args.verbose)message("Loading transcript initial expression data.\n");
trExp = new TranscriptExpression(args.getS("expFileName"), GUESS);
if(trExp->getM() != M){
error("Main: Number of transcripts in the alignment file and the expression file are different: %ld vs %ld\n",M,trExp->getM());
return 1;
}
}
}
//}}}
timer.split(0,'m');
//}}}
// Estimating probabilities {{{
bool analyzeReads = false;
if(args.isSet("lenMu") && args.isSet("lenSigma")){
readD.setLength(args.getD("lenMu"),args.getD("lenSigma"));
}else{
analyzeReads = true;
}
if(args.flag("uniform")){
if(args.verbose)message("Using uniform read distribution.\n");
readD.initUniform(M,trInfo,trSeq,args.flag("veryVerbose"));
}else{
if(args.verbose)message("Estimating non-uniform read distribution.\n");
readD.init(M,trInfo,trSeq,trExp,args.flag("unstranded"),args.flag("veryVerbose"));
if(args.flag("veryVerbose"))message(" ReadDistribution initialization done.\n");
analyzeReads = true;
}
if(args.isSet("numNoiseMismatches")){
readD.setLowProbMismatches(args.getL("numNoiseMismatches"));
}
// fill in "next" fragment:
// Counters for all, Good Alignments; and weird alignments
long observeN, pairedGA, firstGA, secondGA, singleGA, weirdGA, allGA, pairedBad;
bool storedValidA = false;
long RE_noEndInfo, RE_weirdPairdInfo, RE_nameMismatch;
long maxAlignments = 0;
if(args.isSet("maxAlignments") && (args.getL("maxAlignments")>0))
maxAlignments = args.getL("maxAlignments");
// start counting (and possibly estimating):
observeN = pairedGA = firstGA = secondGA = singleGA = weirdGA = pairedBad = 0;
RE_noEndInfo = RE_weirdPairdInfo = RE_nameMismatch = 0;
ns_parseAlignment::readNextFragment(samData, curF, nextF);
while(ns_parseAlignment::readNextFragment(samData,curF,nextF)){
R_INTERUPT;
if( !(curF->first->core.flag & BAM_FUNMAP) ){
// (at least) The first read was mapped.
if( curF->paired ) {
// Fragment's both reads are mapped as a pair.
// Check mates' names.
if((ns_parseAlignment::readNameCmp(bam1_qname(curF->first), bam1_qname(curF->second))==0) ||
(args.flag("mateNamesDiffer"))){
pairedGA++;
}else{
pairedBad++;
if(RE_nameMismatch == 0){
warning("Paired read name mismatch: %s %s\n",bam1_qname(curF->first), bam1_qname(curF->second));
}
RE_nameMismatch++;
if(RE_nameMismatch>10)break;
}
}else {
if (curF->first->core.flag & BAM_FPAIRED) {
// Read was part of pair (meaning that the other is unmapped).
if (curF->first->core.flag & BAM_FREAD1) {
firstGA++;
} else if (curF->first->core.flag & BAM_FREAD2) {
secondGA++;
} else weirdGA ++;
} else {
// Read is single end, with valid alignment.
singleGA++;
}
}
// Unless pairedBad>0 the alignment is valid.
// If excludeSingletons is set, only use paired alignment and alignments of single-end reads.
if((!storedValidA) &&
(((!args.flag("excludeSingletons")) && (pairedBad == 0)) ||
(pairedBad + firstGA + secondGA + weirdGA == 0))){
validAF->copyFragment(curF);
storedValidA=true;
}
}
// Next fragment is different.
if(ns_parseAlignment::nextFragDiffers(curF, nextF, args.flag("mateNamesDiffer"))){
Ntotal++;
allGA = singleGA + pairedGA + firstGA +secondGA+ weirdGA;
if( allGA == 0 ){ // No good alignment.
// Just in case:
storedValidA=false;
pairedBad = 0;
continue;
}
Nmap ++;
if(weirdGA)RE_noEndInfo++;
if((singleGA>0) && (pairedGA>0)) RE_weirdPairdInfo++;
// If it's good uniquely aligned fragment/read, add it to the observation.
if(( allGA == 1) && analyzeReads && (pairedBad == 0) && storedValidA){
if(readD.observed(validAF))observeN++;
}else if(maxAlignments && (allGA>maxAlignments)) {
// This read will be ignored.
ignoredReads.insert(bam1_qname(curF->first));
ignoredMaxAlignments++;
Nmap --;
}else if(args.flag("excludeSingletons") && (pairedGA + singleGA == 0)){
// When excluding singletons only alignments of full pair or single-end read count.
ignoredReads.insert(bam1_qname(curF->first));
ignoredSingletons++;
Nmap --;
}
pairedGA = firstGA = secondGA = singleGA = weirdGA = pairedBad = 0;
storedValidA = false;
}
}
if(RE_nameMismatch>10){
error("Names of paired mates didn't match at least 10 times.\n"
" Something is possibly wrong with your data or the reads have to be renamed.\n");
return 1;
}
message("Reads: all(Ntotal): %ld mapped(Nmap): %ld\n",Ntotal,Nmap);
if(args.verbose)message(" %ld reads were used to estimate empirical distributions.\n",observeN);
if(ignoredMaxAlignments>0)message(" %ld reads are skipped due to having more than %ld alignments.\n",ignoredMaxAlignments, maxAlignments);
if(ignoredSingletons>0)message(" %ld reads skipped due to having just single mate alignments.\n",ignoredSingletons);
if(RE_noEndInfo)warning(" %ld reads that were paired, but do not have \"end\" information.\n (is your alignment file valid?)", RE_noEndInfo);
if(RE_weirdPairdInfo)warning(" %ld reads that were reported as both paired and single end.\n (is your alignment file valid?)", RE_weirdPairdInfo);
readD.writeWarnings();
if(args.flag("veryVerbose"))timer.split(0,'m');
// Normalize read distribution:
if(args.flag("veryVerbose"))message("Normalizing read distribution.\n");
readD.normalize();
if(args.isSet("distributionFileName")){
readD.logProfiles(args.getS("distributionFileName"));
}
timer.split(0,'m');
// }}}
// Writing probabilities: {{{
// Re-opening alignment file
if(!ns_parseAlignment::openSamFile(args.args()[0], inFormat, &samData))return 1;
if(args.verbose)message("Writing alignment probabilities.\n");
double prob,probNoise,minProb;
prob = probNoise = 0;
set<string> failedReads;
vector<ns_parseAlignment::TagAlignment> alignments;
// Open and initialize output file {{{
ofstream outF(args.getS("outFileName").c_str());
if(!outF.is_open()){
error("Main: Unable to open output file.\n");
return 1;
}
outF<<"# Ntotal "<<Ntotal<<"\n# Nmap "<<Nmap<<"\n# M "<<M<<endl;
outF<<"# LOGFORMAT (probabilities saved on log scale.)\n# r_name num_alignments (tr_id prob )^*{num_alignments}"<<endl;
outF.precision(9);
outF<<scientific;
// }}}
// start reading:
timer.start(1);
bool invalidAlignment = false;
long readC, pairedN, singleN, firstN, secondN, weirdN, invalidN, noN;
readC = pairedN = singleN = firstN = secondN = weirdN = invalidN = noN = 0;
RE_nameMismatch = 0 ;
// fill in "next" fragment:
ns_parseAlignment::readNextFragment(samData, curF, nextF);
while(ns_parseAlignment::readNextFragment(samData,curF,nextF)){
R_INTERUPT;
// Skip all alignments of this read.
if(ignoredReads.count(bam1_qname(curF->first))>0){
DEBUG_AT(" ignore\n");
// Read reads while the name is the same.
while(ns_parseAlignment::readNextFragment(samData,curF,nextF)){
DEBUG_AT(" ignore\n");
if(ns_parseAlignment::nextFragDiffers(curF, nextF, args.flag("mateNamesDiffer")))
break;
}
readC++;
if(args.verbose){ if(progressLog(readC,Ntotal,10,' '))timer.split(1,'m');}
continue;
}
if( !(curF->first->core.flag & BAM_FUNMAP) ){
DEBUG_AT("M");
// (at least) The first read was mapped.
// Check mates' names.
if(curF->paired && (ns_parseAlignment::readNameCmp(bam1_qname(curF->first), bam1_qname(curF->second))!=0) && (!args.flag("mateNamesDiffer"))){
if(RE_nameMismatch == 0){
warning("Paired read name mismatch: %s %s\n",bam1_qname(curF->first), bam1_qname(curF->second));
}
RE_nameMismatch++;
if(RE_nameMismatch>10)break;
invalidAlignment = true;
}else if((!args.flag("excludeSingletons")) || curF->paired || (! (curF->first->core.flag & BAM_FPAIRED))){
// We only calculate probabilties and add alignments if:
// (singletons are not exlucded) OR (it is a proper paired alignments) OR (it is single-end read)
if(readD.getP(curF, prob, probNoise)){
// We calculated valid probabilities for this alignment.
// Add alignment:
alignments.push_back(ns_parseAlignment::TagAlignment(curF->first->core.tid+1, prob, probNoise));
// Update counters:
if( curF->paired ) {
// Fragment's both reads are mapped as a pair.
pairedN++;
DEBUG_AT(" P\n");
}else {
if (curF->first->core.flag & BAM_FPAIRED) {
// Read was part of pair (meaning that the other is unmapped).
if (curF->first->core.flag & BAM_FREAD1) {
firstN++;
DEBUG_AT(" 1\n");
} else if (curF->first->core.flag & BAM_FREAD2) {
secondN++;
DEBUG_AT(" 2\n");
} else {
weirdN ++;
DEBUG_AT(" W\n");
}
} else {
// Read is single end, with valid alignment.
singleN++;
DEBUG_AT(" S\n");
}
}
} else {
// Calculation of alignment probabilities failed.
invalidAlignment = true;
}
}
}else DEBUG_AT("UNMAP\n");
// next fragment has different name
if(ns_parseAlignment::nextFragDiffers(curF, nextF, args.flag("mateNamesDiffer"))){
DEBUG_AT(" last\n");
readC++;
if(args.verbose){ if(progressLog(readC,Ntotal,10,' '))timer.split(1,'m');}
if(!alignments.empty()){
outF<<bam1_qname(curF->first)<<" "<<alignments.size()+1;
minProb = 1;
for(i=0;i<(long)alignments.size();i++){
if(minProb>alignments[i].getLowProb())minProb = alignments[i].getLowProb();
outF<<" "<<alignments[i].getTrId()
// <<" "<<getStrandC(alignments[i].getStrand())
<<" "<<alignments[i].getProb();
}
outF<<" 0 "<<minProb<<endl;
alignments.clear();
}else{
// read has no valid alignments:
if(invalidAlignment){
// If there were invalid alignments, write a mock record in order to keep Nmap consistent.
invalidN++;
outF<<bam1_qname(curF->first)<<" 1 0 0"<<endl;
}else {
noN++;
}
if(args.isSet("failed")){
// Save failed reads.
failedReads.insert(bam1_qname(curF->first));
if(curF->paired)failedReads.insert(bam1_qname(curF->second));
}
}
invalidAlignment = false;
}
}
if(RE_nameMismatch>10){
error("Names of paired mates didn't match at least 10 times.\n"
" Something is possibly wrong with your data or the reads have to be renamed.\n");
return 1;
}
outF.close();
timer.split(0,'m');
if(args.verbose){
message("Analyzed %ld reads:\n",readC);
if(ignoredMaxAlignments>0)message(" %ld ignored due to --limitA flag\n",ignoredMaxAlignments);
if(invalidN>0)message(" %ld had only invalid alignments (see warnings)\n",invalidN);
if(noN>0)message(" %ld had no alignments\n",noN);
message("The rest had %ld alignments:\n",pairedN+singleN+firstN+secondN+weirdN);
if(pairedN>0)message(" %ld paired alignments\n",pairedN);
if(firstN+secondN+weirdN>0)
message(" %ld half alignments (paired-end mates aligned independently)\n",firstN+secondN+weirdN);
if(singleN>0)message(" %ld single-read alignments\n",singleN);
//flushStdout();
messageFlush();
}else {
messageF("Alignments: %ld.\n",pairedN+singleN+firstN+secondN+weirdN);
}
readD.writeWarnings();
if(args.flag("veryVerbose")){
message("Number of weights cached: %ld\n",readD.getWeightNormCount());
}
// Deal with reads that failed to align {{{
if(args.isSet("failed")){
outF.open(args.getS("failed").c_str());
if(outF.is_open()){
for(set<string>::iterator setIt=failedReads.begin(); setIt!=failedReads.end();setIt++)
outF<<*setIt<<endl;
outF.close();
}
} //}}}
// Compute effective length and save transcript info {{{
if(args.isSet("trInfoFileName")){
if(args.verbose)messageF("Computing effective lengths.\n");
trInfo->setEffectiveLength(readD.getEffectiveLengths());
if(! trInfo->writeInfo(args.getS("trInfoFileName"))){
warning("Main: File %s probably already exists.\n"
" Will save new transcript info into %s-NEW.\n",(args.getS("trInfoFileName")).c_str(),(args.getS("trInfoFileName")).c_str());
if(! trInfo->writeInfo(args.getS("trInfoFileName")+"-NEW", true)){ // DO OVERWRITE
warning("Main: Writing into %s failed!.",(args.getS("trInfoFileName")+"-NEW").c_str());
}
}else {
if(args.verbose)message("Transcript information saved into %s.\n",(args.getS("trInfoFileName")).c_str());
}
if(args.verbose)timer.split(0,'m');
} //}}}
// Close, free and write failed reads if filename provided {{{
delete curF;
delete nextF;
delete validAF;
delete trInfo;
delete trSeq;
delete trExp;
samclose(samData);
// }}}
// }}}
if(args.verbose)message("DONE. ");
timer.split(7,'m');
return 0;
}
#ifndef BIOC_BUILD
int main(int argc,char* argv[]){
return parseAlignment(&argc,argv);
}
#endif
namespace ns_parseAlignment {
bool nextFragDiffers(const ns_rD::fragmentP curF, const ns_rD::fragmentP nextF, bool mateNamesDiffer){//{{{
if(readNameCmp(bam1_qname(curF->first), bam1_qname(nextF->first))==0) return false;
if(nextF->paired && mateNamesDiffer && (readNameCmp(bam1_qname(curF->first), bam1_qname(nextF->second))==0)) return false;
return true;
}//}}}
long readNameCmp(const char *str1, const char *str2){//{{{
// Check first character(so that we can look back later).
if(*str1 != *str2)return *str1 - *str2;
while(*str1 || *str2){
if(*str1 != *str2){
// They can differ in last character if its preceeeded by /:_.
if(*str1 && *str2 && (!*(str1+1)) && (!*(str2+1)) &&
((*(str1-1) == '/') || (*(str1-1) == ':') || (*(str1-1) == '_'))){
return 0;
}
return *str1 - *str2;
}
str1++;
str2++;
}
return 0;
}//}}}
bool readNextFragment(samfile_t* samData, ns_rD::fragmentP &cur, ns_rD::fragmentP &next){//{{{
static ns_rD::fragmentP tmpF = NULL;
bool currentOK = true;
// switch current to next:
tmpF = cur;
cur = next;
next = tmpF;
// check if current fragment is valid
if( !cur->first->data || ( *(cur->first->data) == '\0')){
// current fragment is invalid
currentOK = false;
}
// try reading next fragment:
if(samread(samData,next->first)<0){
// read failed: set next reads name to empty string
*(next->first->data) = '\0';
return currentOK;
}
// Read proper pairs OR pairs with both mates unmapped into one fragment.
if((next->first->core.flag & BAM_FPROPER_PAIR) ||
((next->first->core.flag & BAM_FPAIRED) &&
(next->first->core.flag & BAM_FUNMAP) &&
(next->first->core.flag & BAM_FMUNMAP))){
next->paired = true;
// Try reading second mate.
if(samread(samData,next->second)<0) next->paired = false;
}else{
next->paired = false;
}
/* Note:
* Relying on BAM_FREAD2 as being the last read of template probably does not work.
*/
return currentOK;
}//}}}
bool setInputFormat(const ArgumentParser &args, string *format){//{{{
if(args.isSet("format")){
*format = args.getLowerS("format");
if((*format =="sam")||(*format == "bam")){
return true;
}
warning("Unknown format '%s'.\n",format->c_str());
}
string fileName = args.args()[0];
string extension = fileName.substr(fileName.rfind(".")+1);
*format = ns_misc::toLower(extension);
if((*format =="sam")||(*format == "bam")){
if(args.verb())message("Assuming alignment file in '%s' format.\n",format->c_str());
return true;
}
message("Unknown extension '%s'.\n",extension.c_str());
error("Couldn't determine the type of input file, please use --format and check your input.\n");
return false;
}//}}}
bool openSamFile(const string &name, const string &inFormat, samfile_t **samFile){//{{{
if(*samFile != NULL)samclose(*samFile);
if(inFormat=="bam") *samFile = samopen(name.c_str(), "rb" , NULL);
else *samFile = samopen(name.c_str(), "r" , NULL);
if(*samFile == NULL){
error("Failed re-reading alignments.\n");
return false;
}
return true;
}//}}}
bool initializeInfoFile(const ArgumentParser &args, samfile_t *samFile, TranscriptInfo **trInfo, long *M){//{{{
if((samFile->header == NULL)||(samFile->header->n_targets == 0)){
if(! args.isSet("trInfoFileName")){
error("Main: alignment file does not contain header, or the header is empty.\n"
" Please either include header in alignment file or provide transcript information file.\n"
" (option --trInfoFile, file should contain lines with <gene name> <transcript name> <transcript length>.\n");
return false;
}else{
if(args.verb())message("Using %s for transcript information.\n",(args.getS("trInfoFileName")).c_str());
if((*trInfo = new TranscriptInfo(args.getS("trInfoFileName"))) && (*trInfo)->isOK()){
*M=(*trInfo)->getM();
}else {
error("Main: Can't get transcript information.\n");
return false;
}
}
}else{
if(args.verbose)message("Using alignments' header for transcript information.\n");
*M = samFile->header->n_targets;
vector<string> trNames(*M);
vector<long> trLengths(*M);
for(long i=0;i<*M;i++){
trNames[i] = samFile->header->target_name[i];
trLengths[i] = samFile->header->target_len[i];
}
*trInfo = new TranscriptInfo();
if(! (*trInfo)->setInfo(vector<string>(*M,"none"), trNames, trLengths)){
error("TranscriptInfo not initialized.\n");
return false;
}
}
return true;
}//}}}
} // namespace ns_parseAlignment
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