Commit 785d096b authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 2.6.1d+dfsg

parent 830c815a

CHANGES.md

+10 −0
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STAR 2.6.1c 2018/11/16

======================



* Fixed the problem causing BAM sorting error with large number of threads and small ulimit -n (github.com/alexdobin/STAR/issues/512).

* Fixed the bug causing inconsistent output for mate1/2 in the Unmapped files (github.com/alexdobin/STAR/issues/222).

* Fixed the non-thread safe error/exit (github.com/alexdobin/STAR/issues/514), and non-safe file size check (github.com/alexdobin/STAR/issues/516)

* Many thanks to Paul Menzel for helping to track and fix these problems.





STAR 2.6.1c 2018/10/17

======================



* Enforced the consistent choice of supplementary chimeric alignments for overlapping mates.





STAR 2.6.1b 2018/09/06

======================

extras/doc-latex/parametersDefault.tex

+1 −1
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@@ -715,7 +715,7 @@ 
  \optLine{int{\textgreater}=0: the score range for multi-mapping chimeras below the best chimeric score. Only works with --chimMultimapNmax {\textgreater} 1} 

\optName{chimNonchimScoreDropMin}

  \optValue{20}

  \optLine{int{\textgreater}=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read lenght has to be smaller than this value} 

  \optLine{int{\textgreater}=0: to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be smaller than this value}

\optName{chimOutJunctionFormat}

  \optValue{0}

  \optLine{int: formatting type for the Chimeric.out.junction file}

source/BAMbinSortByCoordinate.cpp

+7 −4
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@@ -16,11 +16,14 @@ void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, st 
        string bamInFile=dirBAMsort+to_string(it)+"/"+to_string((uint) iBin);

        ifstream bamInStream;

        bamInStream.open(bamInFile.c_str(),std::ios::binary | std::ios::ate);//open at the end to get file size

        uint s1=bamInStream.tellg();

        if (s1>0)

        {

        int64 s1=bamInStream.tellg();

        if (s1>0)         {

            bamInStream.seekg(std::ios::beg);

            bamInStream.read(bamIn+bamInBytes,s1);//read the whole file

        } else if (s1<0) {

            ostringstream errOut;

            errOut << "EXITING because of FATAL ERROR: failed reading from temporary file: " << dirBAMsort+to_string(it)+"/"+to_string((uint) iBin);

            exitWithError(errOut.str(),std::cerr, P.inOut->logMain, 1, P);

        };

        bamInBytes += bamInStream.gcount();

        bamInStream.close();
@@ -29,7 +32,7 @@ void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, st 
    if (bamInBytes!=binS) {

        ostringstream errOut;

        errOut << "EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: ";

        errOut << binS <<"   "<< bamInBytes <<"   "<< iBin <<"\n";

        errOut << "Expected bin size=" <<binS <<" ; size on disk="<< bamInBytes <<" ; bin number="<< iBin <<"\n";

        exitWithError(errOut.str(),std::cerr, P.inOut->logMain, 1, P);

    };

source/BAMoutput.cpp

+2 −1
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@@ -4,6 +4,7 @@ 
#include <pthread.h>

#include "serviceFuns.cpp"

#include "ThreadControl.h"

#include "streamFuns.h"



BAMoutput::BAMoutput (int iChunk, string tmpDir, Parameters &Pin) : P(Pin){//allocate bam array
@@ -23,7 +24,7 @@ BAMoutput::BAMoutput (int iChunk, string tmpDir, Parameters &Pin) : P(Pin){//all 
    for (uint ii=0;ii<nBins;ii++) {

        binStart[ii]=bamArray+bamArraySize/nBins*ii;

        binBytes[ii]=0;

        binStream[ii]=new ofstream((bamDir +"/"+to_string(ii)).c_str());    //open temporary files

        binStream[ii]=&ofstrOpen((bamDir +"/"+to_string(ii)).c_str(), ERROR_OUT, P);    //open temporary files

        binTotalN[ii]=0;

        binTotalBytes[ii]=0;

    };

source/ErrorWarning.cpp

+4 −2
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@@ -3,10 +3,12 @@ functions that handle errors and warnings 
*/

#include "ErrorWarning.h"

#include "TimeFunctions.h"

#include "GlobalVariables.h"



void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2, int errorInt, Parameters &P) {

    time_t timeCurrent;

    time( &timeCurrent);

    if (P.runThreadN>1) pthread_mutex_lock(&g_threadChunks.mutexError);

    if (streamOut1.good()) {

        streamOut1 << "\n" << messageOut << endl << timeMonthDayTime(timeCurrent) <<" ...... FATAL ERROR, exiting\n"  <<flush;

    };
@@ -14,6 +16,6 @@ void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2, 
        streamOut2 << "\n" << messageOut << endl << timeMonthDayTime(timeCurrent) <<" ...... FATAL ERROR, exiting\n"  <<flush;

    };

    delete P.inOut; //to close files



//     if (P.runThreadN>1) pthread_mutex_unlock(&g_threadChunks.mutexError);

    exit(errorInt);

};