Eric Coissac
620646d412
fix: validate inputs and fix coordinate offsets in pattern matching
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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
438893d910
refactor: improve FASTQ error messages with explicit filenames
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The options system now tracks explicit file paths via a new accessor and functional option. This filename is threaded through the FASTQ parser chain to replace generic source references in fatal error messages, providing clearer, file-specific diagnostics without altering core parsing logic or test suites.
2026-08-19 16:47:36 +02:00
Eric Coissac
07cdd6f758
debug obimultiplex
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bug option obimultiplex
2025-11-06 15:43:13 +01:00
Eric Coissac
13ff892ac9
Patch type mismatch in apat C library
2025-04-23 16:14:10 +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
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
a812fe8b72
debug of obimultiplex
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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
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Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
2024-05-30 08:27:24 +02:00
Eric Coissac
017030bcce
Add obiminion first version
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Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
2024-05-14 08:16:12 +02:00
coissac
7bd073ccd4
First version of obisplit and patch a bug in the new workers API
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Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
2024-03-03 11:16:24 -04:00
coissac
8d77cc4133
Change path of the obitools pkg
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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
2023-11-29 12:14:37 +01:00
coissac
d23a911080
Change the way sequence definition are managed. They are now when present stored as an attribute
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Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
2023-10-05 07:21:12 +02:00
coissac
d437fba535
Doc change
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Former-commit-id: 5cd4547147804f887ad699d4886702545584ba32
2023-08-27 17:06:36 +02:00
coissac
3f69fa41d6
Patch a bug for multiple amplicon per sequence.
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Former-commit-id: b252d2de8e1a85d65c2951aa1958ee038e35741d
2023-03-31 15:10:25 +02:00
coissac
988ae79989
Optimize memory allocation of the apat algorithms
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Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede
2023-03-28 19:37:05 +07:00
coissac
d5e84ec676
rename goutils to obiutils
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Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
2023-03-24 10:25:12 +07:00
coissac
57474214e7
Patch excessive log in obimultiplex and an error in detecting the tag.
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Former-commit-id: e6f427ac743cae373247a15bf49b0a27273b2569
2023-03-23 11:40:24 +07:00
coissac
d09011fac2
Finalyse the obimultiplex with indels
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Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85
2023-03-21 22:01:02 +07:00
coissac
27d6c60e25
Add the possibility to look for patterns allowing indels.
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Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
2023-03-20 15:28:24 +07:00
coissac
29563aa94e
Rename the Length methods Len to follow GO standart
2022-11-17 11:09:58 +01:00
coissac
f6735a634e
Correctly patch the memory leak related to the apatsequence
2022-09-12 15:19:46 +02:00
coissac
3e40ae9d52
Patch a memory leak in apat sequence
2022-08-21 13:40:20 +02:00
coissac
2e7c1834b0
Big change iin the data model, and a first version of obiuniq
2022-02-21 19:00:23 +01:00
coissac
b9da72d379
Adds finalizer to ApatSequence
2022-01-24 22:54:41 +01:00
coissac
251d3be923
Add automatic garbage collection on ApatPattern
2022-01-24 17:26:30 +01:00
coissac
4551df08b1
Adds a reader for NGS filter files and change some API for the apat library
2022-01-18 13:09:32 +01:00
coissac
5753723618
Code refactoring
2022-01-14 17:17:54 +01:00
coissac
b9b9c0f179
Patch module name from oa2 to obitools
2022-01-13 23:43:01 +01:00
coissac
f53bf1b804
First commit
2022-01-13 23:27:39 +01:00
Eric Coissac
coissac