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812 Commits 13 Branches 41 Tags
f727ae930f3508ca80581b6647ee83109cc89e5b
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59 Commits
Author SHA1 Message Date
Eric Coissac 620646d412 fix: validate inputs and fix coordinate offsets in pattern matching 
Introduce explicit input validation and a `(-1, -1, -1)` sentinel return value to signal invalid or unreliable matches. Add pre-call length checks and early returns to prevent panics during indel relocation. Fix an index offset bug in coordinate calculation by preserving the original fragment position before applying alignment deltas. Update match filtering to enforce reliability checks only on successfully relocated alignments. Comprehensive tests validate edge cases, boundary constraints, and error thresholds.
 2026-08-19 17:25:44 +02:00
Eric Coissac d17a9520b9 work on obiclean chimera detection 2025-10-20 17:29:47 +02:00
Eric Coissac 5a3705b6bb Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands. 2025-03-25 16:44:46 +01:00
Eric Coissac 8671285d02 add the --min-sample-count option to obiclean. 2025-02-24 08:48:31 +01:00
Eric Coissac 51d11aa36d Changes to be committed: 
modified:   pkg/obialign/alignment.go
	modified:   pkg/obialign/pairedendalign.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obipairing/pairing.go
 2025-02-23 17:37:56 +01:00
Eric Coissac fb6f857d8c Update the computation of the consensus quality score 2025-02-23 15:16:31 +01:00
Eric Coissac ef05d4975f Upadte the scoring schema of obipairing 2025-02-21 22:41:34 +01:00
Eric Coissac d29a56dcbf Changes to be committed: 
modified:   Release-notes.md
	modified:   pkg/obialign/pairedendalign.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/biosequence.go
	modified:   pkg/obitools/obipairing/pairing.go
 2024-11-27 09:56:22 +01:00
Eric Coissac 2b4a633c30 EndGapFree alignments 2024-09-24 15:52:12 +02:00
Eric Coissac 05bf2bfd6c Add option related to agrep match on obigrep and obiannotate 2024-09-09 16:52:13 +02:00
Eric Coissac 65ae82622e correction of several small bugs 2024-09-03 06:08:07 -03:00
Eric Coissac 373464cb06 On development genome skim tools 2024-08-30 11:17:33 +02:00
Eric Coissac 31bfc88eb9 Patch a bug on writing to stdout, and add clearer error on openning data files 2024-08-13 09:45:28 +02:00
Eric Coissac c1f03cb1f6 Switch to faster json library go-json and sonic 
Former-commit-id: ab9b4723f1dcf79fe5c073fff4d86f4f6969edfd
 2024-06-23 00:36:08 +02:00
Eric Coissac 93f9dcb95f Reducing memory allocation events 
Former-commit-id: c94e79ba116464504580fc397270ead154063971
 2024-06-22 22:32:31 +02:00
Eric Coissac e6b87ecd02 Reduce memory allocation events 
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
 2024-06-22 21:01:53 +02:00
Eric Coissac a812fe8b72 debug of obimultiplex 
Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e
 2024-06-18 23:38:33 +02:00
Eric Coissac dd9307a4cd Swich to the system min and max functions and remove the version from obiutils 
Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
 2024-05-30 08:27:24 +02:00
Eric Coissac 017030bcce Add obiminion first version 
Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
 2024-05-14 08:16:12 +02:00
Eric Coissac 9e63013bc2 Correction on obiformat of bug leading to partial parsing and add godocs 
Former-commit-id: b27105355f1a330eedf6eaa72c8ac94f06806c28
 2024-05-07 10:54:12 +02:00
coissac 37c3e16d5d Adds the option --pairing-scale to obipairing 
Former-commit-id: c60416708467f5e818e70e08b3c512014b6212f0
 2023-12-07 12:28:16 +01:00
coissac 8d77cc4133 Change path of the obitools pkg 
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
 2023-11-29 12:14:37 +01:00
coissac b556e045e5 Adds option to tune the pairing of the sequences in obipairing and some stats to the results 
Former-commit-id: a6cf9cb4d4ab20a433a2534fd7d11cd3ca8ebbaa
 2023-11-24 12:29:37 +01:00
coissac ec31ae86b9 Adds some stats in obiparing about fast align results 
Former-commit-id: 44f6d6538e759dd7dc1db068a812957f6b20f50d
 2023-11-24 10:57:10 +01:00
coissac ce66b0af2f Patch a bug in the pair-end alignement in case of equality between scores. 
Former-commit-id: bbdb761a98b76f2421d1f0a72960e72b13b6e626
 2023-11-24 09:59:29 +01:00
coissac 3f8c0d6a2f Replace MakeBioSequence call by NewBioSequence call, 
Implements a new file format guesser
Adds some more API doc


Former-commit-id: 9837bf1c28beca6ddb599b367f93548950ba83c1
 2023-08-30 19:59:46 +02:00
coissac 2a11adb346 Add some doc and switch to the parallel gzip library 
Former-commit-id: 2c1187001f989ba3de5895f516d4c8b54d52a4c4
 2023-08-25 14:36:38 +02:00
coissac 63dc67f344 add debuging log 
Former-commit-id: 7543d12838463bd9d9bcb365e5e6772b51daa5ec
 2023-06-07 17:47:58 +02:00
coissac d5e84ec676 rename goutils to obiutils 
Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
 2023-03-24 10:25:12 +07:00
coissac d09011fac2 Finalyse the obimultiplex with indels 
Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85
 2023-03-21 22:01:02 +07:00
coissac 27d6c60e25 Add the possibility to look for patterns allowing indels. 
Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
 2023-03-20 15:28:24 +07:00
coissac 4117cbdd08 Stabilize the obipairing output. whant run twice on the same dataset results are identical 2023-02-05 11:06:31 +01:00
coissac 39b47a32bf Complement on the doc 2023-01-27 10:49:28 +01:00
coissac cfddc78161 Patch an aligment bug on obipairing 2023-01-25 13:22:56 +01:00
coissac 20b16c0ba1 Force sequence reading to produce lowercase sequences. 
Adds two columns to the obiclean ratio csv file
 2022-11-22 15:06:09 +01:00
coissac 29563aa94e Rename the Length methods Len to follow GO standart 2022-11-17 11:09:58 +01:00
coissac f674200a6e FastLCS with maxError=-1 is equivalent to FullLCS. 2022-11-16 09:57:36 +01:00
coissac 340579f6d7 New version of LCS computation, with abug on alignment length patched patched 2022-11-15 08:21:46 +01:00
coissac 0f99f9a6ba First trial of a fastest LCS implementation 2022-11-14 07:42:15 +01:00
coissac 6429f24c57 Accellerate a bit LCS computation 2022-10-27 17:30:55 +02:00
coissac 8aa323dad5 Add a first version of obitag the successor of ecotag 2022-10-26 13:16:56 +02:00
coissac f8df48338d Several bug in annotation management 2022-10-12 23:01:47 +02:00
coissac ebefa28cc0 Patch memory error related to []byte pool 2022-09-28 14:28:37 +02:00
coissac 5dd835d3e7 A first functional version of obiclean 2022-08-20 18:01:07 +02:00
coissac a07d348aea small change 2022-07-31 21:52:04 +02:00
coissac 656eda1f73 A fiirst version of LCS score function 2022-03-07 16:37:21 +01:00
coissac abcf02e488 Start to use leveled log 2022-02-24 12:14:52 +01:00
coissac 2e7c1834b0 Big change iin the data model, and a first version of obiuniq 2022-02-21 19:00:23 +01:00
coissac 64676db3f4 Connect the command line options to the algorithm of obipairing 2022-01-16 17:30:30 +01:00
coissac 576a9f4d2d A global version of a Slice pool 2022-01-16 00:21:42 +01:00