Commit 609e6279 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tests: update following previous commit

see #4725
parent ebb09977
!NO_EXTRA:
!LAUNCH: ../../tools/align -m 1 -i 2 -j 1 -x $VIDJIL_DATA/trd-dd2-dd3.fa $VIDJIL_DIR/germline/homo-sapiens/TRDD.fa
!LAUNCH: ../../tools/align -m 1 -i 3 -j 1 -x $VIDJIL_DATA/trd-dd2-dd3.fa $VIDJIL_DIR/germline/homo-sapiens/TRDD.fa
$ Load correct sequences
1:TRDD2.01_0//0_TRDJ1.01 .*trd-dd2-dd3.fa
......
......@@ -3,11 +3,11 @@
$ Segment only 2 reads, because we do not look for incomplete recombinations
1:junction detected in 2 reads
$ TRDV3*01-TRDD3*01 reported as "UNSEG only V/5'"
$ TRDV3*01-TRDD3*01 (x2) reported as "UNSEG only V/5'"
1:UNSEG only V/5' .*-> .* 2
$ TRDD2*01-TRDJ1*01 reported as "UNSEG only J/3'"
1:UNSEG only J/3' .*-> .* 2
$ TRDD2*01-TRDJ1*01 (x3) reported as "UNSEG only J/3'"
1:UNSEG only J/3' .*-> .* 3
$ TRDD2*01-TRDD3*01 reported as "UNSEG too few V/J"
1:UNSEG too few V/J.*-> .* 2
$ TRDD2*01-TRDD3*01 (x3) reported as "UNSEG too few V/J"
1:UNSEG too few V/J.*-> .* 3
!LAUNCH: $VIDJIL_DIR/$EXEC -w 10 -e 20 --all -g $VIDJIL_DIR/germline $VIDJIL_DATA/trd-dd2-dd3.fa
$ Segment 6 reads, thanks to -i
1:junction detected in 6 reads
$ Segment 8 reads
1:junction detected in 8 reads
$ 4 reads are detected on TRD+ (with -w 10, otherwise the reads are too short)
1: TRD[+] .*->.* 4
$ 6 reads are detected on TRD+ (with -w 10, otherwise the reads are too short)
1: TRD[+] .*->.* 6
!LAUNCH: $VIDJIL_DIR/$EXEC -K --all -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/homo-sapiens/TRDV.fa -V $VIDJIL_DIR/germline/homo-sapiens/TRDD2+up.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDD3+down.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDJ.fa $VIDJIL_DATA/trd-dd2-dd3.fa ; cat out/trd-dd2-dd3.affects
$ Segment all 8 reads, thanks to TRDD2 and TRDD3
1: junction detected in 8 reads .100..
$ Segment all 10 reads, thanks to TRDD2 and TRDD3
1: junction detected in 10 reads .100..
$ Find the good number of 20-windows
1:windows up to 20bp
......
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