9d93a68b3a
Change setup for the blast filtering before exonerate
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Former-commit-id: 139685eca58c1fb2272854dee31de3821c54af80
Former-commit-id: dc5c345ce72e9895cbdcc3321499b869040a24da
2022-02-17 18:41:27 +01:00
2ff6ff3308
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
2018-11-20 16:02:23 +01:00
04ea0f110d
Allows for reporting
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Former-commit-id: af7999b0f3c69be9c796799813950adbdb0fb0e8
Former-commit-id: f8a6f2a26c58a02aa6d076bd3005a02f906de82a
2016-10-20 09:31:54 -03:00
1ac0af03c2
Patch the new ycf1 specific parameters
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Former-commit-id: 66f848b351a6b8186ff03a7059aa167f39ed29a1
Former-commit-id: fd4260434739725ff967138089eaeeb013812784
2016-10-09 07:19:35 -03:00
8156d5dd2f
Add specific exonerate parameters for ycf1
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Former-commit-id: c956dde7ad2183b72fe5221333876747db97b361
Former-commit-id: 5ddf35ea93eadadecb063277afd513e8ae73e559
2016-10-09 07:11:20 -03:00
e4f3081fa8
Switch to the speedup mode because of the slow down imposed by the new
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exonarate parametters
Former-commit-id: 30f2caea735460bcc4dfa61adde72d7da2fb6f2e
Former-commit-id: 0537c77f5bc16d766b3cbd668dcd1e1711140937
2016-10-06 12:35:32 -03:00
405631f527
cds go_test bug fixed
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Former-commit-id: f73133dca83d02a0c223e98a3ac82fdb0d03c5ae
Former-commit-id: 3db7c0037f7c109f4479490480d4323a55206c6a
2015-11-13 22:37:22 +01:00
d55d5f65a9
default PASS1_SPEEDUP set to 0
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Former-commit-id: 38d036b8626c4595e734669d7c120905d1cd0698
Former-commit-id: 5e6fe77559323483bcbb133521acc6382c252d5e
2015-11-08 18:52:59 +01:00
8dab2d56b2
CDS detector added
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Former-commit-id: 93fac7a70052d06c2a12bf8af59820c653edd31b
Former-commit-id: 0869fdad0f550941a0f78f1e4c57f4fcdb3f6076
2015-11-08 14:28:05 +01:00
