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If proteins are looked for without stop adds an extra option

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PASS1_LOOK_FOR_PSEUDO allowing for searching with stop in a second time
(Pseudogene search).

The PASS1_ALLOW_STOP is set back to 0 and the new PASS1_LOOK_FOR_PSEUDO
is set to 1

Former-commit-id: 318327af6bdc3fbdfbe7f438ff7cbea22863a0ab
Former-commit-id: a130baf2b1c3bf1158d367d3633b02600f04674a
This commit is contained in:
Eric Coissac
2018-11-20 16:02:23 +01:00
parent a040adb132
commit 2ff6ff3308
2 changed files with 14 additions and 2 deletions
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3
detectors/cds/params/default
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@@ -44,7 +44,8 @@ AssignUndef PASS1_SUBMAT $ModelsDir/blosum62.mat
# pass1: cluster selection parameters
#
AssignUndef PASS1_MAX_SPAN 10000
AssignUndef PASS1_ALLOW_STOP 1
AssignUndef PASS1_ALLOW_STOP 0
AssignUndef PASS1_LOOK_FOR_PSEUDO 1
#
# extension parameters