Function fillTempLineArray

samblaster.cpp:1145–1168

template <bool excludeSecondaries>
int fillTempLineArray(splitLine_t * block, state_t * state, int mask, bool flagValue)
{
    // Count the secondaries we have for this read (if any), and store their ptrs into an array.
    int count = 0;
    for (splitLine_t * line = block; line != NULL; line = line->next)
    {
        // For all the ones that are the current read of interest....
        // Check if they are a primary or complementary alignment.
        if (checkFlag(line, mask) == flagValue && !(excludeSecondaries && isSecondaryAlignment(line)))
        {
            // Add the ptr to this line to the sort array.
            // If it won't fit, double the array size.
            if (count >= state->splitterArrayMaxSize)
            {
                state->splitterArrayMaxSize *= 2;
                state->splitterArray = (splitLine_t **)(realloc(state->splitterArray,
                                                                state->splitterArrayMaxSize * sizeof(splitLine_t *)));
            }
            state->splitterArray[count] = line;
            count += 1;
        }
    }
    return count;
}

void markSplitterUnmappedClipped(splitLine_t * block, state_t * state, int mask, bool flagValue)
{