Commit 858b8570 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tests: testing -u

parent 2956e626
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -u $VIDJIL_DIR/data/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
$ The proper unsegmentation cause is given
1: UNSEG too short -> .* 1
1: UNSEG strand -> .* 1
1: UNSEG too few V/J -> .* 3
1: UNSEG only V/5' -> .* 1
1: UNSEG only J/3' -> .* 1
1: UNSEG ambiguous -> .* 1
1: UNSEG too short w -> .* 1
$ The UNSEG ambiguous read is reported in the .UNSEG_ambiguous.fa file (-u)
1: >ambiguous .* UNSEG ambiguous
$ The UNSEG too few V/J reads are *not* reported in any .fa file (-u)
0: >too_few_vj-..* UNSEG too few V/J
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -u $VIDJIL_DIR/data/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -uuu $VIDJIL_DIR/data/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
$ Only one sequence is segmented, but it is too small for a window (too short w)
1: junction detected in 1 reads
......@@ -13,7 +13,7 @@ $ The proper unsegmentation cause is given
1: UNSEG ambiguous -> .* 1
1: UNSEG too short w -> .* 1
$ The proper unsegmentation cause is given in the .unsegmented.vdj.fa file
$ The proper unsegmentation cause is given in the .unsegmented.vdj.fa file (-uuu)
1: >too_short .* UNSEG too short
1: >strand .* UNSEG strand
3: >too_few_vj-..* UNSEG too few V/J
......
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