C++ SamFile::ReadBamIndex方法代码示例

bool BamProcessor::init (const ContalignParams& p)
{
    read_cnt_ = proc_cnt_ = toolongs_ = unaligned_cnt_ = fail_cnt_ = nomd_cnt_ = realigned_cnt_ = modified_cnt_ = pos_adjusted_cnt_ = 0;
    log_diff_ = log_matr_ = log_base_ = false;

    p_ = &p;

    if (!*p.inbam ())
        ers << "Input file name not specified" << Throw;

    limit_ = p.limit ();
    skip_ = p.skip ();

    infile_.OpenForRead (p.inbam ());
    if (!infile_.IsOpen ())
        ers << p.inbam () << ThrowEx (FileNotFoundRerror);

    bool index_ok = false;
    if (*p.bamidx ())
    {
        index_ok = infile_.ReadBamIndex (p.bamidx ());
        if (!index_ok)
            warn << "Unable to open specified BAM index: " << p.bamidx () << ". Default index will be attempted" <<  std::endl;
    }
    if (!index_ok)
    {
        try
        {
            index_ok = infile_.ReadBamIndex ();
        }
        catch (std::exception& e)
        {
            // for some reason not converted into return status by libStatGen
        }
        if (!index_ok)
            warn << "Unable to open default BAM index for " << p.inbam () << std::endl;
    }
    if (*p.refname () || p.refno () != -1)
    {
        if (!index_ok)
            ers << "Reference section specified, but the BAM index could not be open." << Throw;
        if (*p.refname ())
        {
            if (p.endpos () != 0)
            {
                infile_.SetReadSection (p.refname (), p.begpos (), p.endpos ());
                info << "Read section set : " << p.refname () << ": " << p.begpos () << "-" << p.endpos () << std::endl;
            }
            else
            {
                infile_.SetReadSection (p.refname ());
                info << "Read section set : " << p.refname () << std::endl;
            }
        }
        else
        {
            if (p.endpos () != 0)
            {
                info << "Read section set : ref# " << p.refno () << ": " << p.begpos () << "-" << p.endpos () << std::endl;
                infile_.SetReadSection (p.refno (), p.begpos (), p.endpos ());
            }
            else
            {
                info << "Read section set : ref# " << p.refno () << std::endl;
                infile_.SetReadSection (p.refno ());
            }
        }
    }
    if (*p.outbam ())
    {
        if (!p.overwrite () && file_exists (p.outbam ()))
            ers << "Output file " << p.outbam () << " exists. Use --ov key to allow overwriting" << Throw;
        outfile_.OpenForWrite (p.outbam ());
        if (!outfile_.IsOpen ())
            ers << "Unable to open output file " << p.outbam () << std::endl;
    }
    if (*p.logfname ())
    {
        if (!p.overwrite () && file_exists (p.logfname ()))
            ers << "Log file " << p.logfname () << " exists. Use --ov key to allow overwriting" << Throw;
        logfile_.open (p.logfname (), std::fstream::out);
        if (!logfile_.is_open ())
            ers << "Unable to open log file " << p.logfname () << std::endl;

        time_t t = time (NULL);
        logfile_ << "Context-aware realigner log\nStarted at " << asctime (localtime (&t)) << "\nParameters:\n";
        logfile_ << *(p.parameters_);
        logfile_ << std::endl;
        log_base_ = p.logging ("base");
        log_diff_ = p.logging ("diff");
        log_matr_ = p.logging ("matr");
    }
    band_width_ = p.bwid ();

    switch (p.algo ())
    {
        case ContalignParams::TEMPL:
        {
            matrix_.configure (genstr::nucleotides.symbols (), genstr::nucleotides.size (), genstr::NegUnitaryMatrix <int, 4>().values ());
            gap_cost_.configure (p.gip (), p.gep ());
//.........这里部分代码省略.........

void testIndex(BamIndex& bamIndex)
{
    assert(bamIndex.getNumMappedReads(1) == 2);
    assert(bamIndex.getNumUnMappedReads(1) == 0);
    assert(bamIndex.getNumMappedReads(0) == 4);
    assert(bamIndex.getNumUnMappedReads(0) == 1);
    assert(bamIndex.getNumMappedReads(23) == -1);
    assert(bamIndex.getNumUnMappedReads(23) == -1);
    assert(bamIndex.getNumMappedReads(-1) == 0);
    assert(bamIndex.getNumUnMappedReads(-1) == 2);
    assert(bamIndex.getNumMappedReads(-2) == -1);
    assert(bamIndex.getNumUnMappedReads(-2) == -1);
    assert(bamIndex.getNumMappedReads(22) == 0);
    assert(bamIndex.getNumUnMappedReads(22) == 0);

    // Get the chunks for reference id 1.
    Chunk testChunk;
    SortedChunkList chunkList;
    assert(bamIndex.getChunksForRegion(1, -1, -1, chunkList) == true);
    assert(!chunkList.empty());
    testChunk = chunkList.pop();
    assert(chunkList.empty());
    assert(testChunk.chunk_beg == 0x4e7);
    assert(testChunk.chunk_end == 0x599);

    // Get the chunks for reference id 0.
    assert(bamIndex.getChunksForRegion(0, -1, -1, chunkList) == true);
    assert(!chunkList.empty());
    testChunk = chunkList.pop();
    assert(chunkList.empty());
    assert(testChunk.chunk_beg == 0x360);
    assert(testChunk.chunk_end == 0x4e7);


    // Get the chunks for reference id 2.
    assert(bamIndex.getChunksForRegion(2, -1, -1, chunkList) == true);
    assert(!chunkList.empty());
    testChunk = chunkList.pop();
    assert(chunkList.empty());
    assert(testChunk.chunk_beg == 0x599);
    assert(testChunk.chunk_end == 0x5ea);

    // Get the chunks for reference id 3.
    // There isn't one for this ref id, but still successfully read the file,
    // so it should return true, but the list should be empty.
    assert(bamIndex.getChunksForRegion(3, -1, -1, chunkList) == true);
    assert(chunkList.empty());

    // Test reading an indexed bam file.
    SamFile inFile;
    assert(inFile.OpenForRead("testFiles/sortedBam.bam"));
    inFile.setSortedValidation(SamFile::COORDINATE);
    assert(inFile.ReadBamIndex("testFiles/sortedBam.bam.bai"));
    SamFileHeader samHeader;
    assert(inFile.ReadHeader(samHeader));
    SamRecord samRecord;

    // Test getting num mapped/unmapped reads.
    assert(inFile.getNumMappedReadsFromIndex(1) == 2);
    assert(inFile.getNumUnMappedReadsFromIndex(1) == 0);
    assert(inFile.getNumMappedReadsFromIndex(0) == 4);
    assert(inFile.getNumUnMappedReadsFromIndex(0) == 1);
    assert(inFile.getNumMappedReadsFromIndex(23) == -1);
    assert(inFile.getNumUnMappedReadsFromIndex(23) == -1);
    assert(inFile.getNumMappedReadsFromIndex(-1) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex(-1) == 2);
    assert(inFile.getNumMappedReadsFromIndex(-2) == -1);
    assert(inFile.getNumUnMappedReadsFromIndex(-2) == -1);
    assert(inFile.getNumMappedReadsFromIndex(22) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex(22) == 0);

    assert(inFile.getNumMappedReadsFromIndex("2", samHeader) == 2);
    assert(inFile.getNumUnMappedReadsFromIndex("2", samHeader) == 0);
    assert(inFile.getNumMappedReadsFromIndex("1", samHeader) == 4);
    assert(inFile.getNumUnMappedReadsFromIndex("1", samHeader) == 1);
    assert(inFile.getNumMappedReadsFromIndex("22", samHeader) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex("22", samHeader) == 0);
    assert(inFile.getNumMappedReadsFromIndex("", samHeader) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex("*", samHeader) == 2);
    assert(inFile.getNumMappedReadsFromIndex("unknown", samHeader) == -1);
    assert(inFile.getNumUnMappedReadsFromIndex("unknown", samHeader) == -1);
    assert(inFile.getNumMappedReadsFromIndex("X", samHeader) == 0);
    assert(inFile.getNumUnMappedReadsFromIndex("X", samHeader) == 0);

    // Section -1 = Ref *: 2 records (8 & 10 from testSam.sam that is reflected
    // in the validation.
    assert(inFile.SetReadSection(-1));
    assert(inFile.ReadRecord(samHeader, samRecord));
    validateRead8(samRecord);
    assert(inFile.ReadRecord(samHeader, samRecord));
    validateRead10(samRecord);
    assert(inFile.ReadRecord(samHeader, samRecord) == false);

    // Section 2 = Ref 3: 1 records (9 from testSam.sam that is reflected
    // in the validation.
    assert(inFile.SetReadSection(2));
    assert(inFile.ReadRecord(samHeader, samRecord));
    validateRead9(samRecord);
    assert(inFile.ReadRecord(samHeader, samRecord) == false);

//.........这里部分代码省略.........

//.........这里部分代码省略.........
        PileupElementBaseQCStats::setBaseSum(baseSum);
    }

    if(params)
    {
        inputParameters.Status();
    }

    // Open the file for reading.
    SamFile samIn;
    if(!samIn.OpenForRead(inFile))
    {
        fprintf(stderr, "%s\n", samIn.GetStatusMessage());
        return(samIn.GetStatus());
    }

    samIn.SetReadFlags(requiredFlags, excludeFlags);

    // Set whether or not basic statistics should be generated.
    samIn.GenerateStatistics(basic);

    // Read the sam header.
    SamFileHeader samHeader;
    if(!samIn.ReadHeader(samHeader))
    {
        fprintf(stderr, "%s\n", samIn.GetStatusMessage());
        return(samIn.GetStatus());
    }

    // Open the bam index file for reading if we are
    // doing unmapped reads (also set the read section).
    if(useIndex)
    {
        samIn.ReadBamIndex(indexFile);

        if(unmapped)
        {
            samIn.SetReadSection(-1);
        }

        if(!regionList.IsEmpty())
        {
            myRegionList = ifopen(regionList, "r");
        }
    }

    //////////////////////////
    // Read dbsnp if specified and doing baseQC
    if(((baseQCPtr != NULL) || baseSum) && (!dbsnp.IsEmpty()))
    {
        // Read the dbsnp file.
        IFILE fdbSnp;
        fdbSnp = ifopen(dbsnp,"r");
        // Determine how many entries.
        const SamReferenceInfo& refInfo = samHeader.getReferenceInfo();
        int maxRefLen = 0;
        for(int i = 0; i < refInfo.getNumEntries(); i++)
        {
            int refLen = refInfo.getReferenceLength(i);
            if(refLen >= maxRefLen)
            {
                maxRefLen = refLen + 1;
            }
        }
        
        dbsnpListPtr = new PosList(refInfo.getNumEntries(),maxRefLen);