Function processSAMBlock

samblaster.cpp:1284–1333

}

void processSAMBlock(splitLine_t * block, state_t * state)
{
    idCount += 1;
    // First mark dups and find the discordants.
    // These share a lot of looking at flag bits, so make sense to put together.
    markDupsDiscordants(block, state);
    // Look for splitters.
    // Since this is expensive, don't do it unless the user asked for them.
    if (state->splitterFile != NULL || state->unmappedClippedFile != NULL)
    {
        // Check the first read for splitter.
        markSplitterUnmappedClipped(block, state, FIRST_SEG, true);
        // Check the second read for splitter.
        markSplitterUnmappedClipped(block, state, SECOND_SEG, true);
        // Check for a singleton read
        markSplitterUnmappedClipped(block, state, MULTI_SEGS, false);
    }

    // Now do the output.
    for (splitLine_t * line = block; line != NULL; line = line->next)
    {
        // Do the unmapped file first, as it is not sam, and doesn't sew the line back together.
        if (state->unmappedClippedFile != NULL && line->unmappedClipped && !(state->excludeDups && isDuplicate(line)))
        {
            writeUnmappedClipped(line, state);
            unmapClipCount += 1;
        }

        // Write to the output file.
        if (!(state->removeDups && isDuplicate(line)))
        {
            writeLine(line, state->outputFile);
        }

        // Write to discordant file if appropriate.
        if (state->discordantFile != NULL && line->discordant && !(state->excludeDups && isDuplicate(line)))
        {
            writeLine(line, state->discordantFile);
            discCount += 1;
        }
        // Write to splitter file if appropriate.
        if (state->splitterFile != NULL && line->splitter && !(state->excludeDups && isDuplicate(line)))
        {
            writeSAMlineWithIdNum(line, state->splitterFile);
            splitCount += 1;
        }
    }

    disposeSplitLines(block);
}

///////////////////////////////////////////////////////////////////////////////
// Main Routine with helpers.