obitools4

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V4.3

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Release_4.3.0

Release_4.4.0

Release_4.4.10

Release_4.4.11

Release_4.4.12

Release_4.4.13

Release_4.4.14

Release_4.4.15

Release_4.4.16

Release_4.4.17

Release_4.4.18

Release_4.4.19

Release_4.4.20

Release_4.4.21

Release_4.4.22

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Release_4.4.24

Release_4.4.25

Release_4.4.26

Release_4.4.27

Release_4.4.28

Release_4.4.29

Release_4.4.31

Release_4.4.32

Release_4.4.33

Release_4.4.34

Release_4.4.37

Release_4.4.38

Release_4.4.40

Release_4.4.41

Release_4.4.42

Release_4.4.43

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Release_4.4.45

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Release_4.4.9

f3ddac0f50 Small adjustment coissac 2022-10-27 11:18:44 +02:00
8aa323dad5 Add a first version of obitag the successor of ecotag coissac 2022-10-26 13:16:56 +02:00
e17d1fbca6 Patch the error message stored in sequences by obimultiplex coissac 2022-10-17 21:32:24 +02:00
f8df48338d Several bug in annotation management coissac 2022-10-12 23:01:47 +02:00
aae3398701 Replace the CopyMap function by the MustFillMap and adds a InterfaceToIntMap function coissac 2022-10-12 22:56:38 +02:00
58dbdd8698 requires that father.count > son.count coissac 2022-10-05 09:53:56 +02:00
d9c18ab0b5 Add a reverse complement worker coissac 2022-10-05 09:41:59 +02:00
935fc31982 Adds the new obicomplement command coissac 2022-10-05 09:40:09 +02:00
7873b90902 Patch a bug in obigrep... coissac 2022-10-02 20:52:26 +02:00
65210755cc Patch reading of annotation from stdin coissac 2022-09-29 14:48:05 +02:00
d0f63fda56 add functionalities to the expression predicate evaluations coissac 2022-09-28 16:13:20 +02:00
fe5d8e3340 Patch a bug in ngsfilter reading and sample matching coissac 2022-09-28 14:29:19 +02:00
ebefa28cc0 Patch memory error related to []byte pool coissac 2022-09-28 14:28:37 +02:00
57ba460929 add the obi_mutation attribute to the sequences coissac 2022-09-20 22:03:44 +02:00
da8e3fd7b7 Correct the orientation of the mutation pattern coissac 2022-09-20 22:03:01 +02:00
49b4d97803 Remove HTML escaping to json marshaling coissac 2022-09-20 22:01:52 +02:00
3cd8aabd83 Correct some misspelling in option helps Changes to be committed: modified: pkg/obitools/obiclean/options.go modified: pkg/obitools/obiconvert/options.go coissac 2022-09-20 21:59:38 +02:00
f6735a634e Correctly patch the memory leak related to the apatsequence coissac 2022-09-12 15:19:46 +02:00
448f5f83fa Patch a bug in comparison of attibutes during sequence annotation merging coissac 2022-09-08 07:50:17 +02:00
6b8f4490cf Change obiclean algorithm for a better evaluation of ratio coissac 2022-08-31 20:38:03 +02:00
90ba980de6 correct the gml writer coissac 2022-08-30 10:28:05 +02:00
cd202ba72e Adds of new modules coissac 2022-08-23 15:09:51 +02:00
91c2ce551d Add new modules coissac 2022-08-23 15:09:03 +02:00
d04161a0fb small code refactoring coissac 2022-08-23 15:08:35 +02:00
d2f4919bc8 comment out to option that need to be rethought coissac 2022-08-23 15:07:48 +02:00
989e678f6b refactor code and change algorithm used to read from many files coissac 2022-08-23 15:07:06 +02:00
bdf317819b Code refactoring coissac 2022-08-23 11:12:00 +02:00
57e0966d35 Adds some documentation coissac 2022-08-23 11:11:36 +02:00
4df99cec5b Chang log package coissac 2022-08-23 11:10:04 +02:00
abaede48b5 Refactoring of some code coissac 2022-08-23 11:07:39 +02:00
62968aaa26 patch the Taxid method coissac 2022-08-23 11:06:51 +02:00
1e58c92086 Adds a function to test that a list contains at least one occurrence of an element coissac 2022-08-23 11:06:28 +02:00
5a81525e46 Adds a genbank parser coissac 2022-08-23 11:04:57 +02:00
a71e65963b Modify the .gitignore coissac 2022-08-21 17:53:51 +02:00
31c45bf46f Adds documentation and few methods to the BioSequences coissac 2022-08-21 17:53:19 +02:00
eca1af9957 Patch a bug on the FilterOn method coissac 2022-08-21 15:05:14 +02:00
ad4a861261 Change some comments coissac 2022-08-21 14:47:22 +02:00
10663bf79c Patch an algorithm error on th Annotation Classifier coissac 2022-08-21 14:45:53 +02:00
f1e3a68dc4 improved performance coissac 2022-08-21 13:44:09 +02:00
02f445f02f same as previous commit coissac 2022-08-21 13:43:27 +02:00
34e957d3fb Add an option alowwing to use the pool method instead of the concat method when several input files are specified coissac 2022-08-21 13:43:00 +02:00
844e24b818 Add information on the number of workers in the log coissac 2022-08-21 13:41:58 +02:00
f00456fcf3 Add a second way to merge several batch iterators using the pool method. coissac 2022-08-21 13:41:15 +02:00
3e40ae9d52 Patch a memory leak in apat sequence coissac 2022-08-21 13:40:20 +02:00
9677f531c4 Improved performance and ability to read very long sequences. coissac 2022-08-21 13:38:13 +02:00
5dd835d3e7 A first functional version of obiclean coissac 2022-08-20 18:01:07 +02:00
a07d348aea small change coissac 2022-07-31 21:52:04 +02:00
821abb1395 package obistat debut coissac 2022-07-28 16:52:27 +02:00
b4cabf31fc Correctly print StatsOn values in obiformat style coissac 2022-06-14 10:00:45 +02:00
f0de4d8f28 Finalize the correct merging of statistic of occurrences, in I expect every situation coissac 2022-06-14 09:54:33 +02:00
6b13729eba Adds a test for not pushing empty batch on the output coissac 2022-06-14 09:53:35 +02:00
cf5b4baa54 Small bug in sequence counting on merge coissac 2022-05-30 16:28:59 +02:00
f14860a486 Patch header parting and formatiing coissac 2022-05-27 11:53:29 +03:00
656eda1f73 A fiirst version of LCS score function coissac 2022-03-07 16:37:21 +01:00
62cd1c44dc Corrects some bug in building the sequence filter coissac 2022-02-25 10:36:01 +01:00
011898bd9d A first version of obigrep. Normally fully functionnal, but not fully tested coissac 2022-02-25 07:29:52 +01:00
0a36447e2a Adds the log module coissac 2022-02-24 12:15:36 +01:00
a18745a34d Modify the gitignore coissac 2022-02-24 12:15:09 +01:00
abcf02e488 Start to use leveled log coissac 2022-02-24 12:14:52 +01:00
f18cc034bb add an option alias -O for the old obi format coissac 2022-02-24 07:26:55 +01:00
f5b278f5ec edit .gitignore coissac 2022-02-24 07:09:35 +01:00
eaf65fbcce Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools coissac 2022-02-24 07:08:40 +01:00
2e7c1834b0 Big change iin the data model, and a first version of obiuniq coissac 2022-02-21 19:00:23 +01:00
9737f97084 before big changes coissac 2022-02-18 22:53:09 +01:00
37ce3536e1 New more functionnal version of obiuniq. But it has a memory leak coissac 2022-02-18 10:01:23 +01:00
6067b92e2f Adds the notioon of NA value coissac 2022-02-18 10:00:42 +01:00
aef546dae3 Patch a bug in the recycle method coissac 2022-02-18 10:00:15 +01:00
94457f5116 Creare a reorder method coissac 2022-02-18 09:59:47 +01:00
cb125bb2a4 Adds an error message when no sample can be associated coissac 2022-02-18 09:58:56 +01:00
2636882f9f big bug on subschunk coissac 2022-02-18 09:58:08 +01:00
ce226acac0 Few debug on obidistribute and some progresses on obiunique, but -c and -m options are still not working coissac 2022-02-15 10:49:01 +01:00
3586ecc483 second version of obidistribute and a first buggy version of obiuniq coissac 2022-02-15 00:47:02 +01:00
b931321ba1 Adds the hash option to obidistribute coissac 2022-02-14 09:12:57 +01:00
eb32620bb3 Adds a first version of a new obidistribute command coissac 2022-02-14 00:01:01 +01:00
1544bafde1 Updates modules coissac 2022-02-09 22:03:38 +01:00
bd630ea512 Forget the binary writer coissac 2022-02-09 22:00:38 +01:00
27556ce81f Start of implementing binary file format coissac 2022-02-07 11:57:08 +01:00
d5a1a191f8 update go.sum coissac 2022-02-07 11:54:47 +01:00
b193c3edfe adds the obifind command to gitignore coissac 2022-02-07 11:52:56 +01:00
79fcd98e43 updated go.mod coissac 2022-02-07 11:52:06 +01:00
38e4655f38 Correct for a strange bug... coissac 2022-02-07 11:51:35 +01:00
30d80db02d All an option to limit number of CPU coissac 2022-02-06 18:52:53 +01:00
98a4363d22 obimultiplex saves unassigned sequence coissac 2022-02-01 23:25:19 +01:00
e9cdfd7e03 Make subseq method dealing with qualities coissac 2022-02-01 18:49:32 +01:00
bc1d7b26a9 adds missing file coissac 2022-02-01 18:04:11 +01:00
8dbda68746 Adds the command obimultiplex coissac 2022-02-01 17:31:28 +01:00
76d9309508 Remame PCR struct to PCRSim coissac 2022-01-27 12:13:27 +01:00
b9da72d379 Adds finalizer to ApatSequence coissac 2022-01-24 22:54:41 +01:00
251d3be923 Add automatic garbage collection on ApatPattern coissac 2022-01-24 17:26:30 +01:00
703eb62819 Adds elements to .gitignore coissac 2022-01-18 13:10:56 +01:00
4551df08b1 Adds a reader for NGS filter files and change some API for the apat library coissac 2022-01-18 13:09:32 +01:00
6571296bb2 Add some documentation coissac 2022-01-16 19:53:39 +01:00
64676db3f4 Connect the command line options to the algorithm of obipairing coissac 2022-01-16 17:30:30 +01:00
576a9f4d2d A global version of a Slice pool coissac 2022-01-16 00:21:42 +01:00
e1b7e1761c Change the memory management for thee BuildAlignment function coissac 2022-01-15 19:10:16 +01:00
e8fff6477b Work on iterators and recycling of biosequences coissac 2022-01-14 23:11:36 +01:00
ef66ca4972 Code refactoring coissac 2022-01-14 17:32:12 +01:00
5753723618 Code refactoring coissac 2022-01-14 17:17:54 +01:00
ff40222902 Code reefactoring coissac 2022-01-14 16:10:19 +01:00
45a1765a03 Code refactoring coissac 2022-01-14 15:46:36 +01:00

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