Commit caefe7a9 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tests: update

replay !374, but update with new values
parent 629ada6d
......@@ -5,22 +5,22 @@ $ Germlines are custom
1: custom germlines
$ Parses IGHV.fa germline
1: 104369 bp in 357 sequences
1: 156380 bp in 550 sequences
$ Parses IGHD.fa germline
1: 1070 bp in 44 sequences
$ Parses germline/homo-sapiens/IGHJ.fa
1: 701 bp in 13 sequences
$ Parses IGHJ.fa germline
1: 1034 bp in 19 sequences
$ Find the good index loads
1:custom .* 0.078% l13 k12 .* 0.002% l13 k12
1:custom .* 0.149% l13 k12 .* 0.003% l13 k12
$ Find approximately the good number of sequences for e-value computation
1: approx. 131.. sequences
$ Find the good number of windows in Stanford S22
1: found 10767 windows in 13153 reads
1: found 10769 windows in 13153 reads
$ First clone -- find the good number of reads
2:clone-001--.*--0000008
......
......@@ -4,14 +4,14 @@ $ number of reads and kmers
1:13153 reads, 3020179 kmers
$ k-mers, IGHV
1:13116 .* 1219953 .*IGHV
1:13135 .* 1285374 .*IGHV
$ k-mers, IGHJ
1:37 .* 435550 .*IGHJ
$ k-mers, IGHJ+down
1:18 .* 432827 .*IGHJ.down
$ k-mers, ambiguous
1:53416 .*\\?
1:71163 .*\\?
$ k-mers, unknown
1:1406774 .*_
1:1324958 .*_
!LAUNCH: $VIDJIL_DIR/$EXEC -y 0 -k 14 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
$ Find the good number of windows in Stanford S22 (contiguous seed 14)
1: found 10796 windows in 13152 reads
1: found 10795 windows in 13152 reads
......@@ -7,24 +7,24 @@ $ Find the good number of "too short sequences" for windows of size 100
1: UNSEG too short w -> 0
$ Some reads have shortened or shifted windows
1: SEG changed w -> 1370
1: SEG changed w -> 1924
$ Most changed windows are just shifted
915: w100/-5
360: w100/-10
1255: w100/-5
522: w100/-10
$ Some changed windows are lighlty shortened
63: w95/-10
29: w90/-10
95: w95/-10
48: w90/-10
$ Find the good number of detected sequences (including "too short sequences")
1: junction detected in 13153 reads .100%.
$ Find the good number of windows in Stanford S22
1: found 11836 windows in 13153 reads
1: found 11798 windows in 13153 reads
$ Find the correct number of clones with shifted of shortened windows
1245: "Short or shifted window"
1245: "W50"
1729: "Short or shifted window"
1729: "W50"
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