Function writeSAMlineWithIdNum

samblaster.cpp:528–539

Special version of write line that appends an id number to the output. Used to output splitters.

// Special version of write line that appends an id number to the output.
// Used to output splitters.
void writeSAMlineWithIdNum(splitLine_t * line, FILE * output)
{
    // Unsplit the line.
    unsplitSplitLine(line);
    // Split it two ways to isolate the id field.
    splitSplitLine(line, 2);
    outputString(line->fields[0], output);
    if (isPaired(line)) fprintf(output, "_%d\t", isFirstRead(line) ? 1 : 2);
    else                fprintf(output, "\t");
    outputString(line->fields[1], output);
    fprintf(output, "\n");
}

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// Sequence Map