void SAMOutput::SetSoftClip(T_AlignmentCandidate &alignment,
        T_Sequence &read,
        DNALength hardClipPrefix,
        DNALength hardClipSuffix,
        DNALength &softClipPrefix, 
        DNALength &softClipSuffix) {
    DNALength qStart, qEnd;
    qStart = alignment.QAlignStart();
    qEnd   = alignment.QAlignEnd();

    assert(qStart >= hardClipPrefix);
    softClipPrefix = alignment.QAlignStart() - hardClipPrefix;
    assert(alignment.QAlignEnd() + hardClipSuffix <= read.length);
    softClipSuffix = read.length - hardClipSuffix - alignment.QAlignEnd();
}
void SAMOutput::SetHardClip(T_AlignmentCandidate &alignment, 
        T_Sequence &read,
        DNALength &prefixClip,
        DNALength &suffixClip) {
    //
    // Set the hard clipping assuming the read is in the forward
    // direction.
    //
    prefixClip = alignment.QAlignStart();
    suffixClip = read.length - alignment.QAlignEnd();
    if (alignment.tStrand == 1) {
        //
        // If the read is instead reverse, swap the clipping lengths.
        //
        std::swap(prefixClip, suffixClip);
    }
}
void IntervalOutput::Print(T_AlignmentCandidate &alignment, std::ostream &outFile)
{

    int mapQV = alignment.mapQV;
    int lastBlock = alignment.blocks.size() - 1;
    if (lastBlock < 0) return;

    outFile << alignment.qName << " " << alignment.tName << " " << alignment.score << " "
            << alignment.pctSimilarity << " " << alignment.qStrand << " " << alignment.QAlignStart()
            << " " << alignment.QAlignEnd() << " " << alignment.qLength << " " << alignment.tStrand
            << " " << alignment.TAlignStart() << " "
            << (alignment.tAlignedSeqPos + alignment.tPos + alignment.blocks[lastBlock].tPos +
                alignment.blocks[lastBlock].length)
            << " " << alignment.tLength << " " << mapQV << std::endl;
    //Remove the last four fields from m4 format.
    //<< " " << alignment.nCells << " " << alignment.clusterScore
    //<< " " << alignment.probScore << " "
    //<< alignment.numSignificantClusters
}
void SAMOutput::SetAlignedSequence(T_AlignmentCandidate &alignment, T_Sequence &read,
        T_Sequence &alignedSeq,
        Clipping clipping) {
    //
    // In both no, and hard clipping, the dna sequence that is output
    // solely corresponds to the aligned sequence.
    //
    DNALength clippedReadLength = 0;
    DNALength clippedStartPos   = 0;

    if (clipping == none or clipping == hard) {
        DNALength qStart = alignment.QAlignStart();
        DNALength qEnd   = alignment.QAlignEnd();
        clippedReadLength = qEnd - qStart;
        clippedStartPos   = qStart;
    }
    else if (clipping == soft) {
        clippedReadLength = read.length - read.lowQualityPrefix - read.lowQualitySuffix;
        clippedStartPos = read.lowQualityPrefix;
    }
    else if (clipping == subread) {
        clippedReadLength = read.subreadEnd - read.subreadStart;
        clippedStartPos = read.subreadStart;
    }
    else {
        std::cout <<" ERROR! The clipping must be none, hard, subread, or soft when setting the aligned sequence." << std::endl;
        assert(0);
    }

    //
    // Set the aligned sequence according to the clipping boundaries.
    //
    if (alignment.tStrand == 0) {
        alignedSeq.ReferenceSubstring(read, clippedStartPos, clippedReadLength);
    }
    else {
        T_Sequence subSeq;
        subSeq.ReferenceSubstring(read, clippedStartPos, clippedReadLength);
        subSeq.MakeRC(alignedSeq);
        assert(alignedSeq.deleteOnExit);
    }
}
void SAMOutput::PrintAlignment(T_AlignmentCandidate &alignment,
        T_Sequence &read,
        std::ostream &samFile,
        AlignmentContext &context,
        SupplementalQVList & qvList,
        Clipping clipping,
        bool cigarUseSeqMatch) {

    std::string cigarString;
    uint16_t flag;
    T_Sequence alignedSequence;
    DNALength prefixSoftClip = 0, suffixSoftClip = 0;
    DNALength prefixHardClip = 0, suffixHardClip = 0;

    CreateCIGARString(alignment, read, cigarString, clipping, prefixSoftClip, suffixSoftClip, prefixHardClip, suffixHardClip, cigarUseSeqMatch);
    SetAlignedSequence(alignment, read, alignedSequence, clipping);
    BuildFlag(alignment, context, flag);
    samFile << alignment.qName << "\t" 
            << flag << "\t" 
            << alignment.tName << "\t";   // RNAME
    if (alignment.tStrand == 0) {
      samFile << alignment.TAlignStart() + 1 << "\t"; 
      // POS, add 1 to get 1 based coordinate system
    }
    else {
      samFile << alignment.tLength - (alignment.TAlignStart() + alignment.TEnd()) + 1 << "\t"; // includes - 1 for rev-comp,  +1 for one-based
    }
    samFile << (int) alignment.mapQV << "\t"// MAPQ
            << cigarString << "\t"; // CIGAR
      
      //
      // Determine RNEXT

    std::string rNext;
    rNext = "*";
    /*
    if (context.hasNextSubreadPos == false) {
      rNext = "*";
    }
    else {
      if (context.rNext == alignment.tName) {
        rNext = "=";
      }
      else {
        rNext = context.rNext;
      }
    }
    */
    samFile << rNext << "\t"; // RNEXT
    
    DNALength nextSubreadPos = 0;
    /*
    if (context.hasNextSubreadPos) {
      nextSubreadPos = context.nextSubreadPos + 1;
      }*/
    samFile << nextSubreadPos << "\t"; // RNEXT, add 1 for 1 based
                                           // indexing

    //DNALength tLen = alignment.GenomicTEnd() - alignment.GenomicTBegin();
    //SAM v1.5, tLen is set as 0 for single-segment template
    samFile << 0 << "\t"; // TLEN
    // Print the sequence on one line, and suppress printing the
    // newline (by setting the line length to alignedSequence.length
    (static_cast<DNASequence*>(&alignedSequence))->PrintSeq(samFile, 0);  // SEQ
    samFile << "\t";
    if (alignedSequence.qual.data != NULL && qvList.useqv == 0) {
        alignedSequence.PrintAsciiQual(samFile, 0);  // QUAL
    }
    else {
      samFile <<"*";
    }
    samFile << "\t";
    //
    // Add optional fields
    //
    samFile << "RG:Z:" << context.readGroupId << "\t";
    samFile << "AS:i:" << alignment.score << "\t";

    //
    // "RG" read group Id
    // "AS" alignment score
    // "XS" read alignment start position without counting previous soft clips (1 based) 
    // "XE" read alignment end position without counting previous soft clips (1 based) 
    // "XL" aligned read length 
    // "XQ" query sequence length
    // "XT" # of continues reads, always 1 for blasr 
    // "NM" edit distance 
    // "FI" read alignment start position (1 based) 
    //
    
    DNALength qAlignStart = alignment.QAlignStart();
    DNALength qAlignEnd = alignment.QAlignEnd();

    if (clipping == none) {
      samFile << "XS:i:" << qAlignStart + 1 << "\t";
      samFile << "XE:i:" << qAlignEnd + 1 << "\t";
    }
    else if (clipping == hard or clipping == soft or clipping == subread) {
        DNALength xs = prefixHardClip;
        DNALength xe = read.length - suffixHardClip;
        if (alignment.tStrand == 1) {
            xs = suffixHardClip;
            xe = read.length - prefixHardClip;
        }
        samFile << "XS:i:" << xs + 1 << "\t"; // add 1 for 1-based indexing in sam
        assert(read.length - suffixHardClip == prefixHardClip + alignedSequence.length);
        samFile << "XE:i:" << xe + 1 << "\t";
    }
    samFile << "YS:i:" << read.subreadStart << "\t";
    samFile << "YE:i:" << read.subreadEnd << "\t";
    samFile << "ZM:i:" << read.zmwData.holeNumber << "\t";
    samFile << "XL:i:" << alignment.qAlignedSeq.length << "\t";
    samFile << "XT:i:1\t"; // reads are allways continuous reads, not
                        // referenced based circular consensus when
                        // output by blasr.
    samFile << "NM:i:" << context.editDist << "\t";
    samFile << "FI:i:" << alignment.qAlignedSeqPos + 1;
    // Add query sequence length
    samFile << "\t" << "XQ:i:" << alignment.qLength;

    //
	// Write out optional quality values.  If qvlist does not 
	// have any qv's signaled to print, this is a no-op.
	//
	// First transform characters that are too large to printable ones.
	qvList.FormatQVOptionalFields(alignedSequence);
	qvList.PrintQVOptionalFields(alignedSequence, samFile);

    samFile << std::endl;
}