Commit 78d5cc0f authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.h: macro rename, UNSEG_TOO_SHORT_FOR_WINDOWS

To be too short for the window is just a non-segmentation/non-analysis cause.
parent 58cbb1c4
......@@ -39,15 +39,15 @@ using namespace std;
enum SEGMENTED { DONT_KNOW, SEG_PLUS, SEG_MINUS, UNSEG_TOO_SHORT, UNSEG_STRAND_NOT_CONSISTENT,
UNSEG_TOO_FEW_ZERO, UNSEG_TOO_FEW_V, UNSEG_TOO_FEW_J,
UNSEG_BAD_DELTA_MIN, UNSEG_BAD_DELTA_MAX, UNSEG_AMBIGUOUS, UNSEG_NOISY,
UNSEG_TOO_SHORT_FOR_WINDOW,
TOTAL_SEG_AND_WINDOW,
TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW,
STATS_SIZE } ;
const char* const segmented_mesg[] = { "?", "SEG_+", "SEG_-", "UNSEG too short", "UNSEG strand",
"UNSEG too few (0)", "UNSEG too few V", "UNSEG too few J",
"UNSEG < delta_min", "UNSEG > delta_max", "UNSEG ambiguous",
"UNSEG noisy",
"= SEG, with window",
"= SEG, no window",
"UNSEG too short w",
"SEG",
} ;
class Segmenter {
......
......@@ -54,7 +54,7 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
stats[TOTAL_SEG_AND_WINDOW].insert(read_length) ;
windowsStorage->add(junc, reads->getSequence(), seg->getSegmentationStatus(), seg->segmented_germline);
} else {
stats[TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW].insert(read_length) ;
stats[UNSEG_TOO_SHORT_FOR_WINDOW].insert(read_length) ;
}
if (out_segmented) {
......
......@@ -966,7 +966,7 @@ int main (int argc, char **argv)
ostringstream stream_segmentation_info;
int nb_segmented_including_too_short = we.getNbSegmented(TOTAL_SEG_AND_WINDOW)
+ we.getNbSegmented(TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW);
+ we.getNbSegmented(UNSEG_TOO_SHORT_FOR_WINDOW);
stream_segmentation_info << " ==> segmented " << nb_segmented_including_too_short << " reads"
<< " (" << setprecision(3) << 100 * (float) nb_segmented_including_too_short / nb_total_reads << "%)"
......
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