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9741276a94
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compute the length of the alignment corresponding to the LCS. this allows
accurate computation of distances from LCS where mismatches and indels count
for 1 unit of distance each.
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2011-11-12 06:56:19 +00:00 |
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f98dd1e7e6
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doc
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2011-10-30 12:47:47 +00:00 |
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f13f701f0e
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add doc + patch on subgraph method
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2011-10-30 12:45:00 +00:00 |
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1eda28068c
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cleannin obitools doc
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2011-10-30 05:09:27 +00:00 |
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cc1da327ef
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2011-10-30 05:04:37 +00:00 |
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633a54186f
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cleannin obitools doc
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2011-10-30 05:03:11 +00:00 |
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edb2ee62cd
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cleannin obitools doc
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2011-10-30 05:02:29 +00:00 |
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Céline Mercier
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0617a020bc
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remove build folder from repository
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2011-10-29 09:14:02 +00:00 |
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6e882b57a9
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add a copy of the raw script source to the build directory for helping documentation generation
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2011-10-27 01:10:27 +00:00 |
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c19dfda8d1
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Sphinx documentation
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2011-10-27 01:06:30 +00:00 |
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fa1d496906
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Sphinx documentation
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2011-10-27 01:05:19 +00:00 |
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0ba055b4d3
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Add sphinx extension for documentation
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2011-10-27 01:04:48 +00:00 |
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608878cf75
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Sphinx documentation
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2011-10-27 01:02:20 +00:00 |
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Céline Mercier
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bfd7fa7c8b
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correct documentation
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2011-10-26 11:09:32 +00:00 |
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8dd20d1839
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Sphinx documentation
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2011-10-26 09:48:03 +00:00 |
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a82e406b12
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Sphinx documentation
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2011-10-26 09:39:32 +00:00 |
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bea64faf6a
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switch docstring to sphinx
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2011-10-26 09:37:51 +00:00 |
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0518f5146b
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add a counter variable in the evaluation environment used for modifying attributes, id, definition and sequences
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2011-10-24 13:32:35 +00:00 |
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e34727e7aa
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patch bug in the build of the new sequence
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2011-10-24 08:02:19 +00:00 |
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d409c88284
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Patch a bug with undefined count tag in sequences
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2011-10-07 12:38:54 +00:00 |
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5ef8e0c802
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add an option to specify the quality score of the added N
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2011-10-07 11:11:25 +00:00 |
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1c3fcac632
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Add a new obijoinpairend to join both the direct and reverse reads of a pair end sequencing with an n linker
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2011-10-07 11:00:33 +00:00 |
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ed8106a539
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Add alternative sampling strategy for large sequence file
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2011-10-07 07:32:21 +00:00 |
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Frédéric Boyer
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e03a33488d
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ali2consensus.py initial version
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2011-09-30 15:23:52 +00:00 |
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f6b96188ce
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patch a bug for -a option
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2011-09-23 16:08:03 +00:00 |
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747249f93b
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add _localtaxon attribute to the TaxonomyDump instance
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2011-09-23 14:41:38 +00:00 |
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ef88f843ae
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add _nameidx attribute to TaxonomyDump
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2011-09-23 14:28:49 +00:00 |
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cc336bf5a0
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patch error on count attribute (work around)
|
2011-09-05 13:49:21 +00:00 |
|
Frédéric Boyer
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6ff8005751
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Test
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2011-08-30 12:48:06 +00:00 |
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4ec0566597
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Skip sequence of null length in solexaPairEnd
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2011-08-29 14:53:36 +00:00 |
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496fbebe7d
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removed ecoTaxSpecificityWithErr.py
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2011-07-26 15:05:15 +00:00 |
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f4e6dc1882
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Added Errors and Quorum in ecoTaxSpecificity.py
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2011-07-26 12:58:57 +00:00 |
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078a1c8328
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Add a capacity for taxonomy to manage extension to it through the notion of local taxa
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2011-07-19 06:48:42 +00:00 |
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a0fca4cfd8
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Consider partial match with IUPAC codes as full match for primer detection
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2011-07-15 14:23:06 +00:00 |
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0c792ac886
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Add a new version of freeendgapfullmatch with full match reward for partial matching
with IUPAC code
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2011-07-15 14:19:24 +00:00 |
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0ff107fb19
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Add a new version of freeendgapfullmatch with full match reward for partial matching
with IUPAC code
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2011-07-15 14:18:32 +00:00 |
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3eb15c4b88
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patch the tag file reading
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2011-07-15 12:51:07 +00:00 |
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2a9cd0ddcd
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add two files, ecoTaxSpecificityWithErr.py and ecoTaxSpecificityEx.py
|
2011-06-26 15:13:07 +00:00 |
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01a1b7d801
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patch backtracking of reverse assemble
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2011-06-24 10:18:20 +00:00 |
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12e746f492
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Change the tag description file format. Tag can now be a single tag or a pair of tags separated by a colon.
|
2011-06-18 06:05:22 +00:00 |
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850fac46e0
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2011-06-17 14:57:07 +00:00 |
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ea05affb10
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add categories attribute to determine uniqueness
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2011-06-16 20:42:38 +00:00 |
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253b76c3d3
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add categories attribute to determine uniqueness
|
2011-06-16 20:36:50 +00:00 |
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5d1c12100c
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add categories attribute to determine uniqueness
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2011-06-16 20:33:59 +00:00 |
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450328a78d
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Asking for tags count to a sequence now always success and return 1 by default
|
2011-06-16 20:24:43 +00:00 |
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0b29ecab80
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move the --rank option to the bioseqedittag option set
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2011-06-16 16:51:34 +00:00 |
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f66aaab769
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move the --rank option to the bioseqedittag option set
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2011-06-16 16:51:23 +00:00 |
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9bafa0ed19
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compute sum of count per category and print them as a new column named total
|
2011-06-16 15:02:39 +00:00 |
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4133a16a6a
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completely new implementation of ngsfilter
|
2011-06-15 21:34:04 +00:00 |
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b8d966c641
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simplify code according to the new progressBar feature
|
2011-06-15 21:32:09 +00:00 |
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