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Mise à jour terminée. Pour connaître les apports de la version 13.8.4 par rapport à notre ancienne version vous pouvez lire les "Release Notes" suivantes :
https://about.gitlab.com/releases/2021/02/11/security-release-gitlab-13-8-4-released/
https://about.gitlab.com/releases/2021/02/05/gitlab-13-8-3-released/

Commit 2ecc174b authored by Mikaël Salson's avatar Mikaël Salson
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Test: Test unsegmentation cause with long V and J

parent b43f8672
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Showing with 18 additions and 6 deletions
algo/tests/testSegment.cpp
View file @ 2ecc174b
......@@ -157,6 +157,14 @@ void testSegmentationCause() {
TAP_TEST(! ks.isSegmented(), TEST_KMER_IS_SEGMENTED, "fewJ: " << ks.getKmerAffectAnalyser()->toString());
TAP_TEST(ks.getSegmentationStatus() == UNSEG_TOO_FEW_J, TEST_KMER_SEGMENTATION_CAUSE, "");
nb_checked++;
} else if (data.read(i).label == "seq-fewV2") {
TAP_TEST(! ks.isSegmented(), TEST_KMER_IS_SEGMENTED, "");
TAP_TEST(ks.getSegmentationStatus() == UNSEG_TOO_FEW_V, TEST_KMER_SEGMENTATION_CAUSE, "");
nb_checked++;
} else if (data.read(i).label == "seq-fewJ2") {
TAP_TEST(! ks.isSegmented(), TEST_KMER_IS_SEGMENTED, "fewJ: " << ks.getKmerAffectAnalyser()->toString());
TAP_TEST(ks.getSegmentationStatus() == UNSEG_TOO_FEW_J, TEST_KMER_SEGMENTATION_CAUSE, "");
nb_checked++;
} else if (data.read(i).label == "seq-delta-min-old") {
// This test was a test for delta_min but with the CountKmerAffectAnalyser
// the read is segmented, now. So we keep it, but change the test
......@@ -190,7 +198,7 @@ void testSegmentationCause() {
}
}
TAP_TEST(nb_checked == 11, TEST_KMER_DATA, "");
TAP_TEST(nb_checked == 13, TEST_KMER_DATA, "");
delete multi;
}
......@@ -218,15 +226,15 @@ void testExtractor() {
WindowsStorage *ws = we.extract(&data, multi, 30, labels);
TAP_TEST(we.getNbReads() == 11, TEST_EXTRACTOR_NB_READS, "");
TAP_TEST(we.getNbReads() == 13, TEST_EXTRACTOR_NB_READS, "");
TAP_TEST(we.getNbSegmented(SEG_PLUS) == 4, TEST_EXTRACTOR_NB_SEGMENTED, "segPlus: " << we.getNbSegmented(SEG_PLUS));
TAP_TEST(we.getNbSegmented(SEG_MINUS) == 1, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_TOO_SHORT) == 1, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_STRAND_NOT_CONSISTENT) == 1, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_TOO_FEW_ZERO) == 1, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_TOO_FEW_V) == 1, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_TOO_FEW_J) == 1, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_TOO_FEW_V) == 2, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_TOO_FEW_J) == 2, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_BAD_DELTA_MIN) == 0, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(UNSEG_BAD_DELTA_MAX) == 1, TEST_EXTRACTOR_NB_SEGMENTED, "");
TAP_TEST(we.getNbSegmented(TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW) == 2, TEST_EXTRACTOR_NB_SEGMENTED, "");
......@@ -237,8 +245,8 @@ void testExtractor() {
TAP_TEST(we.getAverageSegmentationLength(UNSEG_TOO_SHORT) == 4, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(UNSEG_STRAND_NOT_CONSISTENT) == 36, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(UNSEG_TOO_FEW_ZERO) == 36, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(UNSEG_TOO_FEW_V) == 36, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(UNSEG_TOO_FEW_J) == 36, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(UNSEG_TOO_FEW_V) == 51, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(UNSEG_TOO_FEW_J) == 55, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(UNSEG_BAD_DELTA_MAX) == 66, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW) == 28.5, TEST_EXTRACTOR_AVG_LENGTH, "");
TAP_TEST(we.getAverageSegmentationLength(TOTAL_SEG_AND_WINDOW) == 48, TEST_EXTRACTOR_AVG_LENGTH, "");
......
data/segmentation.fasta
View file @ 2ecc174b
......@@ -10,8 +10,12 @@ tgtgccacctgggacaggAGTTTCTTATAATAATTC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>seq-fewV
AAAAAAAAAAAAAAAAAAGAATTATTATAAGAAACT
>seq-fewV2
AAAAAAAAAAAAAAAAAAGAATTATTATAAGAAACTCTTTGGCAGTGGAACAACACTGGTTGTCAC
>seq-fewJ
tgtgccacctgggacaggAAAAAAAAAAAAAAAAAA
>seq-fewJ2
tgcaaaatctaattaaaaatgattctgggttctattactgtgccacctgggacaggAAAAAAAAAAAAAAAAAA
>seq-delta-min-old
tgtgccacctgggacaggGAATTATTATAAGAAACTtgtgccacctgggacaggGAATTATTATAAGAAACT
>seq-delta-min
......
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