Commit bd3d663b authored by Mikaël Salson's avatar Mikaël Salson Committed by Mathieu Giraud

stanford{-wall,-json,-w100,}.should-get: All reads are segmented

With Aho-Corasick we now segment them all!
parent c3d3a486
......@@ -8,4 +8,4 @@ $ Most abundant window, twice, fused
1:"id": "CCACCTATTACTGTACCCGGGAGGAACAATATAGCAGCTGGTACTTTGACTTCTGGGGCC".*"reads": \[8, 8\].*"top": 2
$ Windows that are not in the bottom of the distribution
1: "distribution": \{[^}]+ "0.00001": \[9061, 9061\]
1: "distribution": \{[^}]+ "0.00001": \[9062, 9062\]
......@@ -10,7 +10,7 @@ $ Number of reads
1:"total": \[13153\]
$ Number of segmented reads
1:"segmented": \[13152\]
1:"segmented": \[13153\]
$ Most abundant window
1:"id": "CCACCTATTACTGTACCCGGGAGGAACAATATAGCAGCTGGTACTTTGACTTCTGGGGCC".*"reads": \[8\]
......
......@@ -7,10 +7,10 @@ $ 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 -> 1369
1: SEG changed w -> 1370
$ Most changed windows are just shifted
914: w100/-5
915: w100/-5
360: w100/-10
$ Some changed windows are lighlty shortened
......@@ -18,13 +18,13 @@ $ Some changed windows are lighlty shortened
29: w90/-10
$ Find the good number of segmented sequences (including "too short sequences")
1: junction detected in 13152 reads .100%.
1: junction detected in 13153 reads .100%.
$ Find the good number of windows in Stanford S22
1: found 11835 windows in 13152 reads
1: found 11836 windows in 13153 reads
$ Find the correct number of clones with shifted of shortened windows
1244: "Short or shifted window"
1244: "W50"
1245: "Short or shifted window"
1245: "W50"
......@@ -4,7 +4,7 @@
$ The junctions are the reads
1: considering all analyzed reads as windows
1: found 13140 windows in 13152 reads
1: found 13141 windows in 13153 reads
$ Only the first 12 clones have 2 reads
2:clone-012--IGH--0000002
......
......@@ -20,7 +20,7 @@ $ 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 10766 windows in 13152 reads
1: found 10767 windows in 13153 reads
$ First clone -- find the good number of reads
2:clone-001--.*--0000008
......
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