| d858e7f | Peio | 10 October 2012, 08:46:09 UTC | bugfix: clean_reads does not trim left edge | 10 October 2012, 08:46:09 UTC |
| 61b2205 | Peio | 14 September 2012, 10:59:24 UTC | removed raw against cleaned read stats | 14 September 2012, 10:59:24 UTC |
| 8cf148c | Peio | 14 September 2012, 07:17:11 UTC | updated bast2go database configuration. updated tests with new results | 14 September 2012, 07:17:11 UTC |
| 433ff71 | Peio | 13 September 2012, 07:02:08 UTC | bugfix: pipeline does not remove temporary file testfixes: update some test to work with mandatory pl_ in filename | 13 September 2012, 07:02:08 UTC |
| 5e76089 | Peio | 06 June 2012, 12:10:44 UTC | Improve error message when scrapping the file on backbone | 06 June 2012, 12:10:44 UTC |
| 232e5da | Peio | 06 June 2012, 11:16:44 UTC | bugfix. quality filter adds bad made segments | 06 June 2012, 11:16:44 UTC |
| 0670dcc | Peio | 06 June 2012, 10:45:11 UTC | bugfix. when removing adaptors we always choose the longest not overlaping region. | 06 June 2012, 10:45:11 UTC |
| b79d1c8 | Peio | 06 June 2012, 09:21:04 UTC | bugfix. return none when trim limits are 0,0 | 06 June 2012, 09:21:04 UTC |
| 50b8370 | Peio | 06 June 2012, 09:04:43 UTC | added to clean reads the option to keep 5 prime segment in trimming | 06 June 2012, 09:04:43 UTC |
| 0c5fba4 | Peio | 06 June 2012, 09:02:13 UTC | added option to keep 5 prime segments when trimming sequences | 06 June 2012, 09:02:13 UTC |
| dbe6ba7 | Peio | 30 May 2012, 09:53:08 UTC | bugfix. We did not distribute univec nor 454_adapters files | 30 May 2012, 09:53:08 UTC |
| fd098c3 | Peio | 03 May 2012, 11:19:01 UTC | Release of ngs_backbone 1.4 and clean_reads 0.2.3 | 03 May 2012, 11:19:01 UTC |
| da26b85 | Peio | 03 May 2012, 11:18:24 UTC | update cap enzyme utils to adapt to the new snv format | 03 May 2012, 11:18:24 UTC |
| b8ff065 | Peio | 03 May 2012, 11:17:21 UTC | update cap enzyme utils to adapt to the new snv format | 03 May 2012, 11:17:21 UTC |
| afba878 | Peio | 03 May 2012, 09:39:35 UTC | bugfix: correct a test | 03 May 2012, 09:39:35 UTC |
| 691d025 | peio | 03 May 2012, 07:21:10 UTC | Merge branch 'master' of ssh://bioinfo:2203/franklin | 03 May 2012, 07:21:10 UTC |
| e7a9bd8 | peio | 27 April 2012, 12:47:27 UTC | update prepare for mira. prepare input sequences | 27 April 2012, 12:47:27 UTC |
| 62cdf8b | Jose Blanca | 26 April 2012, 15:04:18 UTC | segment merging now accepts to merge close segments | 26 April 2012, 15:04:18 UTC |
| 65aacb5 | Peio | 25 April 2012, 07:35:09 UTC | Merge branch 'master' of ssh://bioinfo:2203/franklin | 25 April 2012, 07:35:09 UTC |
| 8021b4b | Peio | 25 April 2012, 07:35:00 UTC | added some test to _Codegenerator private code generator class | 25 April 2012, 07:35:00 UTC |
| 703959f | peio | 24 April 2012, 09:22:49 UTC | Added script to prepare iassembler to skip first mira run | 24 April 2012, 09:22:49 UTC |
| 1c2a7d0 | Peio | 23 April 2012, 11:43:19 UTC | update .gitignore | 23 April 2012, 11:43:19 UTC |
| 4052362 | Peio | 20 April 2012, 13:00:27 UTC | added a line to fix no handler errros in logging | 20 April 2012, 13:00:27 UTC |
| 26a83af | Peio | 20 April 2012, 07:52:37 UTC | remove clean reads download files from git | 20 April 2012, 07:52:37 UTC |
| d91c21d | Dani Pérez | 20 April 2012, 07:34:51 UTC | delete from git the downloads directory | 20 April 2012, 07:34:51 UTC |
| 1999efd | Peio | 19 April 2012, 08:35:19 UTC | added suffix and prefix to NamedTemporaryDir | 19 April 2012, 08:35:19 UTC |
| fa7a8da | Peio | 02 April 2012, 06:37:49 UTC | update vecscreen blast options | 02 April 2012, 06:37:49 UTC |
| 3e347f3 | Peio | 30 March 2012, 10:48:29 UTC | updated blast to version 2.2.26 | 30 March 2012, 10:48:29 UTC |
| 2ddd38e | Peio | 30 March 2012, 10:40:43 UTC | updated univec to version 7.0 | 30 March 2012, 10:40:43 UTC |
| 5d47cc9 | Peio | 28 March 2012, 12:56:15 UTC | use fhand instead of seq iterator in ctransitive clustering all | 28 March 2012, 12:56:15 UTC |
| 5c4d07c | Peio | 28 March 2012, 09:56:58 UTC | added contig_member mira format file to changin name using naming schema | 28 March 2012, 09:56:58 UTC |
| 08edb9d | Peio | 28 March 2012, 09:40:42 UTC | added option to use not matching seqs to transitive clustering | 28 March 2012, 09:40:42 UTC |
| 98d1684 | Peio | 28 March 2012, 08:11:40 UTC | comment the line to run all test | 28 March 2012, 08:11:40 UTC |
| 9c86181 | Peio | 23 March 2012, 09:09:39 UTC | bugfix: transitive clusters not joining transitive clusters, only pairs into clusters | 23 March 2012, 09:09:39 UTC |
| 57c333e | Peio | 22 March 2012, 11:51:21 UTC | added function to make transitive clusters of sequences using a blast output | 22 March 2012, 11:51:21 UTC |
| 9ce9fa7 | Peio | 21 March 2012, 12:46:51 UTC | vcfparser now accepts version > 4 of vcf | 21 March 2012, 12:46:51 UTC |
| b224349 | Peio | 21 March 2012, 11:48:58 UTC | merged of branch vcf4 | 21 March 2012, 11:48:58 UTC |
| 57f44b0 | Dani Pérez | 21 March 2012, 10:32:08 UTC | bugfix: vcf indexed as gff not as vcf | 21 March 2012, 10:32:08 UTC |
| e53b493 | Dani Pérez | 20 March 2012, 12:52:00 UTC | compress and index vcf after writing it in backbone | 20 March 2012, 12:52:00 UTC |
| 7a35b3a | Dani Pérez | 20 March 2012, 12:51:26 UTC | bugfix: resulting snv of a deleting insert or deletion will be a complex if the length of the alleles is bigger than 1 | 20 March 2012, 12:51:26 UTC |
| fc6b341 | Dani Pérez | 15 March 2012, 12:46:43 UTC | bugfix: we return None snv | 15 March 2012, 12:46:43 UTC |
| 0482563 | Dani Pérez | 15 March 2012, 10:51:29 UTC | bugfix: remove strange alleles caused by new allele quality calculations | 15 March 2012, 10:51:29 UTC |
| e4cf045 | Dani Pérez | 14 March 2012, 09:04:25 UTC | bugfix: old_snv_caller returns two alleles, 'insertion/snp', now returns just one of type 'complex' | 14 March 2012, 09:04:25 UTC |
| 0869c07 | Dani Pérez | 14 March 2012, 07:26:42 UTC | change in vcfwriter header. GC number type from G to '.' | 14 March 2012, 07:26:42 UTC |
| 345a742 | Dani Pérez | 13 March 2012, 11:52:50 UTC | bugfix: close unmapped file when it is None | 13 March 2012, 11:52:50 UTC |
| 2ffeb07 | Dani Pérez | 13 March 2012, 11:51:08 UTC | refactoring. stop -> end: now: stop] and end[ | 13 March 2012, 11:51:08 UTC |
| 0a037df | Dani Pérez | 13 March 2012, 11:37:19 UTC | bugfix: join contiguous snvs in one block | 13 March 2012, 11:37:19 UTC |
| 7aabfcf | Dani Pérez | 08 March 2012, 08:16:35 UTC | Merge branch 'vcf4' of ssh://bioinfo.comav.upv.es:2203/franklin into vcf4 | 08 March 2012, 08:16:35 UTC |
| 0e32bac | Dani Pérez | 08 March 2012, 08:16:15 UTC | bugfix: snvcaller fails when there increase block size tp the left | 08 March 2012, 08:16:15 UTC |
| 8c99435 | Dani Pérez | 07 March 2012, 11:12:31 UTC | update gatk | 07 March 2012, 11:12:31 UTC |
| 078b547 | Peio | 06 March 2012, 14:01:05 UTC | update vcf writer. passed filter markerd with PASS | 06 March 2012, 14:01:05 UTC |
| 1fa6ecd | Peio | 02 March 2012, 14:02:02 UTC | pep 8 compliance | 02 March 2012, 14:02:02 UTC |
| 01507b8 | Peio | 02 March 2012, 13:42:02 UTC | Merge branch 'vcf4' of ssh://bioinfo:2203/franklin into vcf4 | 02 March 2012, 13:42:02 UTC |
| ab3588c | Peio | 02 March 2012, 13:40:32 UTC | docfixes | 02 March 2012, 13:40:32 UTC |
| 7b9dc9c | Dani Pérez | 28 February 2012, 13:46:09 UTC | bugfix: insert in last segments failed | 28 February 2012, 13:46:09 UTC |
| 9829d49 | Dani Pérez | 23 February 2012, 13:05:39 UTC | bugfix: stop_segment was None and tried to make a substrack | 23 February 2012, 13:05:39 UTC |
| 79f2a80 | Dani Pérez | 22 February 2012, 09:44:15 UTC | bugfix: get_alignment section | 22 February 2012, 09:44:15 UTC |
| f7dc55d | Dani Pérez | 15 February 2012, 09:11:53 UTC | bugfixes: snv_block join bug and deletion length calc bug | 15 February 2012, 09:11:53 UTC |
| f8b292e | Peio | 14 February 2012, 11:09:59 UTC | minor changes in tests | 14 February 2012, 11:09:59 UTC |
| 5284ae8 | Dani Pérez | 07 February 2012, 13:56:04 UTC | bugfix: some multiple alignments fail | 07 February 2012, 13:56:04 UTC |
| f180108 | Peio | 24 January 2012, 10:26:55 UTC | update vcf writer to vcf4.1 spec | 24 January 2012, 10:26:55 UTC |
| bf97269 | Peio | 20 January 2012, 13:40:17 UTC | changed the snv caller: Join snvs that shoul be together and changed the vcf output file to version 4.1 | 20 January 2012, 13:40:17 UTC |
| ad8c1e1 | Peio | 19 January 2012, 07:48:45 UTC | improve test input data | 19 January 2012, 07:48:45 UTC |
| 7067442 | Peio | 17 January 2012, 13:29:06 UTC | update snv kind calculator | 17 January 2012, 13:29:06 UTC |
| 9aed932 | Peio | 17 January 2012, 12:09:52 UTC | added test data | 17 January 2012, 12:09:52 UTC |
| d8b7a37 | Peio | 13 January 2012, 13:21:01 UTC | added get_alignment section from pileup_read | 13 January 2012, 13:21:01 UTC |
| 5d69706 | Peio | 13 January 2012, 12:35:49 UTC | first code to get alignments from pileup_read | 13 January 2012, 12:35:49 UTC |
| 9d26ea2 | Peio | 10 January 2012, 08:21:34 UTC | remove print from gff test | 10 January 2012, 08:21:34 UTC |
| 6c4a823 | Peio | 22 December 2011, 11:59:06 UTC | bugfix: make all paths to absolute path to work with multithreading | 22 December 2011, 11:59:06 UTC |
| c94c2f1 | Peio | 22 December 2011, 11:57:19 UTC | start joining the contiguous snvs | 22 December 2011, 11:57:19 UTC |
| f58e76b | Peio | 15 December 2011, 13:53:59 UTC | use gzip file to store unmapped_reads | 15 December 2011, 13:53:59 UTC |
| f0c49e4 | Peio | 15 December 2011, 11:26:13 UTC | bugfix: unmapped_fpath not well formed | 15 December 2011, 11:26:13 UTC |
| 12113f5 | Peio | 14 December 2011, 12:29:53 UTC | update bam stats to acept unmapped reads file | 14 December 2011, 12:29:53 UTC |
| d38899b | Peio | 14 December 2011, 11:36:46 UTC | config option to keep or remove unmapped reads from the resulting bam | 14 December 2011, 11:36:46 UTC |
| b9df922 | Peio | 05 December 2011, 12:38:35 UTC | update releases date in docs | 05 December 2011, 12:38:35 UTC |
| 9679cad | Peio | 05 December 2011, 12:16:31 UTC | added clean_reads downloads to gitignore | 05 December 2011, 12:16:31 UTC |
| 81b3aca | Peio | 05 December 2011, 12:14:46 UTC | uploaded doc downlowds pages to show latest releases | 05 December 2011, 12:14:46 UTC |
| b2c2c36 | Peio | 05 December 2011, 11:52:44 UTC | bump ngs_backbone and clean_reads version | 05 December 2011, 11:52:44 UTC |
| f470001 | Peio | 05 December 2011, 11:50:48 UTC | minor cosmetic bugfixes | 05 December 2011, 11:50:48 UTC |
| 0116fd6 | Peio | 28 November 2011, 11:09:44 UTC | bugfix: update some code to newer classes | 28 November 2011, 11:09:44 UTC |
| ad422ca | Peio | 28 November 2011, 09:39:23 UTC | remove old code in mapping | 28 November 2011, 09:39:23 UTC |
| 0f7d791 | Peio | 28 November 2011, 09:38:04 UTC | added tmpdir to mapping analysis | 28 November 2011, 09:38:04 UTC |
| fbd3b89 | Peio | 22 November 2011, 12:26:51 UTC | bugfix: vcfparser doen not detect diferente alleles in count | 22 November 2011, 12:26:51 UTC |
| b6b4be2 | Peio | 22 November 2011, 11:43:58 UTC | bugfix: vcfparser doen not detect diferente alleles in count | 22 November 2011, 11:43:58 UTC |
| 0e25486 | Peio | 22 November 2011, 07:35:17 UTC | vcfparser: not count , and . values in allele count | 22 November 2011, 07:35:17 UTC |
| 94943d8 | Peio | 22 November 2011, 07:29:51 UTC | vcfparser: not count , and . values in allele count | 22 November 2011, 07:29:51 UTC |
| c22a773 | Peio | 21 November 2011, 11:49:54 UTC | vcfparser added | 21 November 2011, 11:49:54 UTC |
| 2f7e751 | Peio | 16 November 2011, 11:21:20 UTC | Merge branch 'master' of ssh://bioinfo:2203/franklin | 16 November 2011, 11:21:20 UTC |
| 87ca15b | Peio | 16 November 2011, 11:21:11 UTC | changes in read_map | 16 November 2011, 11:21:11 UTC |
| 43fa8d2 | Dani Pérez | 14 November 2011, 13:08:12 UTC | changed the way we named to features in gffSeqwriter | 14 November 2011, 13:08:12 UTC |
| a10de9f | Peio | 14 November 2011, 08:19:00 UTC | Merge branch 'master' of ssh://bioinfo:2203/franklin | 14 November 2011, 08:19:00 UTC |
| f38334e | Peio | 14 November 2011, 08:17:19 UTC | change ssr output writes to use 1 base coordinates | 14 November 2011, 08:17:19 UTC |
| 19f7dd3 | Dani Pérez | 11 November 2011, 09:23:38 UTC | Merge branch 'master' of ssh://bioinfo.comav.upv.es:2203/franklin | 11 November 2011, 09:23:38 UTC |
| fdc4ca7 | Dani Pérez | 11 November 2011, 09:23:31 UTC | update gff to fit with previos changes in how we deal with gff attributes | 11 November 2011, 09:23:31 UTC |
| ece12c5 | Peio | 11 November 2011, 09:12:31 UTC | change orf strand from from attributes tu feature | 11 November 2011, 09:12:31 UTC |
| 2ea9b00 | Peio | 09 November 2011, 12:14:27 UTC | remove 'name' from gff attributes | 09 November 2011, 12:14:27 UTC |
| 3f484fa | Peio | 09 November 2011, 12:13:20 UTC | Revert "remove 'name' from gff attributes" This reverts commit 31a7c7b1fab23c815200b9a1c52048394d21eee3. | 09 November 2011, 12:13:20 UTC |
| f7524c4 | Peio | 09 November 2011, 12:13:01 UTC | remove 'name' from gff attributes | 09 November 2011, 12:13:01 UTC |
| 9e8b52c | Peio | 09 November 2011, 12:04:54 UTC | remove 'name' from gff attributes | 09 November 2011, 12:04:54 UTC |
| 1deb6e7 | Peio | 24 October 2011, 08:13:12 UTC | bugfix: diff stats does not have same bin_edges | 24 October 2011, 08:13:12 UTC |
