| 05d08d1 | Mark Fiers | 09 August 2012, 04:33:10 UTC | better colors & linestyles | 09 August 2012, 04:33:10 UTC |
| ce7e1ea | Mark Fiers | 02 August 2012, 00:25:12 UTC | lowered the --minLen default value | 02 August 2012, 00:25:12 UTC |
| 58c2e31 | Mark Fiers | 30 July 2012, 08:19:52 UTC | second test set | 30 July 2012, 08:19:52 UTC |
| 57ccf6c | Mark Fiers | 30 July 2012, 08:19:23 UTC | minor fixes | 30 July 2012, 08:19:23 UTC |
| daebce3 | Mark Fiers | 28 June 2012, 09:46:56 UTC | changed COLLIST to a matplotlib.colors.LinearSegmentedColormap | 28 June 2012, 09:46:56 UTC |
| b1ce859 | Mark Fiers | 28 June 2012, 09:17:45 UTC | bugfix - allows for more than five regions - colorlist problem | 28 June 2012, 09:17:45 UTC |
| f6a91c8 | Mark Fiers | 28 June 2012, 08:45:05 UTC | bugfix - now accepts only a list of regions | 28 June 2012, 08:45:05 UTC |
| 0c90140 | Mark Fiers | 28 June 2012, 08:42:53 UTC | bugfix - now accepts only a list of regions | 28 June 2012, 08:42:53 UTC |
| 4871d75 | Mark Fiers | 28 June 2012, 08:41:58 UTC | bugfix - now accepts only a list of regions | 28 June 2012, 08:41:58 UTC |
| 5757025 | Mark Fiers | 28 June 2012, 08:39:03 UTC | accepts a list of regions in a region file | 28 June 2012, 08:39:03 UTC |
| 48d73bd | Mark Fiers | 28 June 2012, 08:03:18 UTC | started work on hagfish_cumulcovplot_reg to read regions from a file - not finished | 28 June 2012, 08:03:18 UTC |
| 74078f5 | Mark Fiers | 28 June 2012, 07:46:23 UTC | better name - not so confusing | 28 June 2012, 07:46:23 UTC |
| 346557c | Mark Fiers | 28 June 2012, 04:47:08 UTC | added a flag to manipulate the samtools -f flag used by hagfish | 28 June 2012, 04:47:08 UTC |
| 45bddcf | Mark Fiers | 20 June 2012, 20:24:58 UTC | removed superfluous debuggin | 20 June 2012, 20:24:58 UTC |
| 281239d | Mark Fiers | 20 June 2012, 04:59:11 UTC | added a list of colors | 20 June 2012, 04:59:11 UTC |
| 5058fbd | Mark Fiers | 20 June 2012, 04:55:53 UTC | do comparative cumulative coverage plots | 20 June 2012, 04:55:53 UTC |
| 8212176 | Mark Fiers | 13 June 2012, 23:50:12 UTC | better labels | 13 June 2012, 23:50:12 UTC |
| 8c55b76 | Mark Fiers | 13 June 2012, 23:33:13 UTC | minor fixes | 13 June 2012, 23:33:13 UTC |
| 40dd823 | Mark Fiers | 13 June 2012, 23:32:36 UTC | minor changes | 13 June 2012, 23:32:36 UTC |
| 85c3a11 | Mark Fiers | 13 June 2012, 23:32:27 UTC | much improved graphs * not plotting score density anymore * added indication of the fraction of the genome containing NNNs to the cumulative plot * much different coverage distribution plot. | 13 June 2012, 23:32:27 UTC |
| 7217504 | Mark Fiers | 12 June 2012, 09:30:36 UTC | better name | 12 June 2012, 09:30:36 UTC |
| e72b611 | Mark Fiers | 12 June 2012, 09:14:43 UTC | somewhat updated version of _blockcompplot | 12 June 2012, 09:14:43 UTC |
| 3949321 | Mark Fiers | 12 June 2012, 09:13:43 UTC | uses tag | 12 June 2012, 09:13:43 UTC |
| 4462848 | Mark Fiers | 12 June 2012, 09:13:32 UTC | minor fixes | 12 June 2012, 09:13:32 UTC |
| 7b7a5a6 | Mark Fiers | 12 June 2012, 08:50:18 UTC | minor cleanup | 12 June 2012, 08:50:18 UTC |
| 43ceb5a | Mark Fiers | 12 June 2012, 08:48:05 UTC | better use of 'tag' & library names in title & outputfilename | 12 June 2012, 08:48:05 UTC |
| d0a02c9 | Mark Fiers | 12 June 2012, 08:43:42 UTC | uses tag in title & plot name | 12 June 2012, 08:43:42 UTC |
| 10ce58c | Mark Fiers | 12 June 2012, 08:43:31 UTC | uses 'tag' for title & plot name | 12 June 2012, 08:43:31 UTC |
| 6a7da0c | Mark Fiers | 12 June 2012, 04:27:08 UTC | equivalent of cplot2 - but for comparative plots | 12 June 2012, 04:27:08 UTC |
| d2a9a93 | Mark Fiers | 12 June 2012, 04:23:01 UTC | merged | 12 June 2012, 04:23:01 UTC |
| 5426b8b | Mark Fiers | 12 June 2012, 04:20:53 UTC | minor changes | 12 June 2012, 04:20:53 UTC |
| 8b757f0 | Mark Fiers | 11 June 2012, 09:03:09 UTC | Merge branch 'master' of ssh.github.com:mfiers/hagfish | 11 June 2012, 09:03:09 UTC |
| e64edf5 | Mark Fiers | 11 June 2012, 09:01:40 UTC | minor fix | 11 June 2012, 09:01:40 UTC |
| c06b3b1 | Mark Fiers | 28 May 2012, 01:43:21 UTC | more flexible in sequence identifiers - now accepts '|' in a seqid | 28 May 2012, 01:43:21 UTC |
| 4aef287 | Mark Fiers | 21 May 2012, 05:18:59 UTC | corresponding with the --ymax fix | 21 May 2012, 05:18:59 UTC |
| 135702d | Mark Fiers | 21 May 2012, 05:18:18 UTC | removed some deprecated code | 21 May 2012, 05:18:18 UTC |
| 79d79f2 | Mark Fiers | 21 May 2012, 05:17:59 UTC | excutable | 21 May 2012, 05:17:59 UTC |
| d1c535d | Mark Fiers | 21 May 2012, 05:17:37 UTC | minor fix - problem with --ymax | 21 May 2012, 05:17:37 UTC |
| a3bb3e5 | Mark Fiers | 21 May 2012, 02:20:17 UTC | renamed | 21 May 2012, 02:20:17 UTC |
| dca6926 | Mark Fiers | 21 May 2012, 02:19:41 UTC | move demo_data to test | 21 May 2012, 02:19:41 UTC |
| b43c792 | Mark Fiers | 21 May 2012, 02:17:27 UTC | allow SAM input with the -S flag | 21 May 2012, 02:17:27 UTC |
| 0822adc | Mark Fiers | 21 May 2012, 02:17:07 UTC | execute a demo run | 21 May 2012, 02:17:07 UTC |
| 13cc7bb | Mark Fiers | 21 May 2012, 02:16:51 UTC | ignore demo run directory | 21 May 2012, 02:16:51 UTC |
| 021451d | Mark Fiers | 18 May 2012, 15:19:22 UTC | demo data | 18 May 2012, 15:19:22 UTC |
| 995aec4 | Mark Fiers | 18 May 2012, 14:58:19 UTC | generate wiggle formatted plots | 18 May 2012, 14:58:19 UTC |
| a0abfc8 | Mark Fiers | 16 May 2012, 16:29:20 UTC | ignore stuff | 16 May 2012, 16:29:20 UTC |
| 854370e | Mark Fiers | 16 May 2012, 16:28:33 UTC | minor fix - range expects an integer | 16 May 2012, 16:28:33 UTC |
| 34daf4e | Mark Fiers | 16 May 2012, 16:28:19 UTC | fasta sequence - demo data | 16 May 2012, 16:28:19 UTC |
| 9db5f2d | Mark Fiers | 19 April 2012, 22:11:02 UTC | plot gaps in the blockplots | 19 April 2012, 22:11:02 UTC |
| 0af221b | Mark Fiers | 19 April 2012, 22:10:48 UTC | fixed a problem - did not output if nothing is in the ok category | 19 April 2012, 22:10:48 UTC |
| 3a350cb | Mark Fiers | 17 April 2012, 04:14:04 UTC | cplot score is now black | 17 April 2012, 04:14:04 UTC |
| 0f0b6f5 | Mark Fiers | 17 April 2012, 04:13:38 UTC | minor fixes | 17 April 2012, 04:13:38 UTC |
| bd6896c | Mark Fiers | 17 April 2012, 04:08:43 UTC | cplot & cplot2 look better now - visualizing regions with gaps | 17 April 2012, 04:08:43 UTC |
| 7ac15d2 | Mark Fiers | 17 April 2012, 04:00:21 UTC | hagfish_cplot2 looks much better now | 17 April 2012, 04:00:21 UTC |
| a117420 | Mark Fiers | 17 April 2012, 03:06:32 UTC | fixed BAM @SQ header parsing problem | 17 April 2012, 03:06:32 UTC |
| d219447 | Mark Fiers | 12 April 2012, 04:20:32 UTC | merged | 12 April 2012, 04:20:32 UTC |
| 3686892 | Mark Fiers | 12 April 2012, 04:17:19 UTC | improved reporting | 12 April 2012, 04:17:19 UTC |
| ceaa185 | Mark Fiers | 12 April 2012, 04:14:23 UTC | ongoing work | 12 April 2012, 04:14:23 UTC |
| f68df07 | Mark Fiers | 12 April 2012, 04:14:17 UTC | identifies NNN regions (gaps) | 12 April 2012, 04:14:17 UTC |
| 1dcaa04 | Mark Fiers | 12 April 2012, 04:13:29 UTC | alternative version of hagfish_cplot - plots both the icp and rcp | 12 April 2012, 04:13:29 UTC |
| 3a3d8bd | Mark Fiers | 13 March 2012, 20:32:26 UTC | minor updates | 13 March 2012, 20:32:26 UTC |
| 29cc598 | Mark Fiers | 13 March 2012, 20:32:18 UTC | hagfish_report for ALL reference sequences in one go | 13 March 2012, 20:32:18 UTC |
| a0befc6 | Mark Fiers | 06 March 2012, 22:49:33 UTC | minor fixes | 06 March 2012, 22:49:33 UTC |
| d9194cb | Mark Fiers | 06 March 2012, 21:18:15 UTC | moved docs to the wiki | 06 March 2012, 21:18:15 UTC |
| 9a7a12b | Mark Fiers | 06 March 2012, 21:18:09 UTC | forgot to add this | 06 March 2012, 21:18:09 UTC |
| 1c388fb | Mark Fiers | 27 November 2011, 07:56:03 UTC | syncing | 27 November 2011, 07:56:03 UTC |
| e2d5332 | Mark Fiers | 02 November 2011, 20:35:30 UTC | Merge branch 'master' of ssh.github.com:mfiers/hagfish * 'master' of ssh.github.com:mfiers/hagfish: jinja template for hagfish report | 02 November 2011, 20:35:30 UTC |
| dfd4bd1 | Mark Fiers | 02 November 2011, 20:33:23 UTC | jinja template for hagfish report | 02 November 2011, 20:33:23 UTC |
| 5442421 | Mark Fiers | 02 November 2011, 20:23:34 UTC | Merge branch 'master' of ssh.github.com:mfiers/hagfish * 'master' of ssh.github.com:mfiers/hagfish: changed categories | 02 November 2011, 20:23:34 UTC |
| 4806449 | Mark Fiers | 02 November 2011, 20:20:30 UTC | fix in gff output | 02 November 2011, 20:20:30 UTC |
| 2ca9539 | Mark Fiers | 02 November 2011, 20:17:18 UTC | changed categories | 02 November 2011, 20:17:18 UTC |
| 769300c | Mark Fiers | 02 November 2011, 03:54:45 UTC | Merge branch 'master' of ssh.github.com:mfiers/hagfish | 02 November 2011, 03:54:45 UTC |
| e433ae9 | Mark Fiers | 02 November 2011, 03:54:30 UTC | minor fix | 02 November 2011, 03:54:30 UTC |
| 3157b39 | Mark Fiers | 02 November 2011, 03:50:46 UTC | tiny bugfix | 02 November 2011, 03:50:46 UTC |
| 883cbeb | Mark Fiers | 02 November 2011, 03:49:14 UTC | Merge branch 'master' of ssh.github.com:mfiers/hagfish * 'master' of ssh.github.com:mfiers/hagfish: do not export cat 0 (no information) flattens a hagfish coverage plot into regions of four categories restored the README | 02 November 2011, 03:49:14 UTC |
| 36a4470 | Mark Fiers | 02 November 2011, 03:47:08 UTC | do not export cat 0 (no information) | 02 November 2011, 03:47:08 UTC |
| b096b92 | Mark Fiers | 02 November 2011, 03:46:46 UTC | flattens a hagfish coverage plot into regions of four categories | 02 November 2011, 03:46:46 UTC |
| ec5946b | Mark Fiers | 02 November 2011, 03:28:11 UTC | it appears that not all gzip objects like the "with" statement | 02 November 2011, 03:28:11 UTC |
| 7245dbb | Mark Fiers | 02 November 2011, 02:30:52 UTC | restored the README | 02 November 2011, 02:30:52 UTC |
| 9d84903 | Mark Fiers | 02 November 2011, 01:59:14 UTC | Merge branch 'master' of ssh.github.com:mfiers/hagfish * 'master' of ssh.github.com:mfiers/hagfish: lots of improvements & rearrangements - reporting function is in the works lots of improvements & rearrangements - reporting function is in the works about to remove the cumulative plot - it's very confusing about to remove the cumulative plot - it's very confusing moved np_load & np_savez to a separate lib utilities to replace np.savez / np.load - since these scannot handle large files (or so it seems) preliminary works with new data structure hagfish_coverage_combine now works with the new data structure generate report | 02 November 2011, 01:59:14 UTC |
| d52fd7e | Mark Fiers | 02 November 2011, 01:58:45 UTC | small fixes | 02 November 2011, 01:58:45 UTC |
| 09778cb | Mark Fiers | 02 November 2011, 01:51:16 UTC | lots of improvements & rearrangements - reporting function is in the works | 02 November 2011, 01:51:16 UTC |
| f02e2b3 | Mark Fiers | 01 November 2011, 19:55:10 UTC | lots of improvements & rearrangements - reporting function is in the works | 01 November 2011, 19:55:10 UTC |
| 15723f7 | Mark Fiers | 01 November 2011, 00:50:08 UTC | about to remove the cumulative plot - it's very confusing | 01 November 2011, 00:50:08 UTC |
| 786f118 | Mark Fiers | 01 November 2011, 00:48:43 UTC | about to remove the cumulative plot - it's very confusing | 01 November 2011, 00:48:43 UTC |
| e386f3d | Mark Fiers | 31 October 2011, 18:48:55 UTC | moved np_load & np_savez to a separate lib | 31 October 2011, 18:48:55 UTC |
| ebf47c7 | Mark Fiers | 31 October 2011, 18:47:30 UTC | utilities to replace np.savez / np.load - since these scannot handle large files (or so it seems) | 31 October 2011, 18:47:30 UTC |
| 0ecef6f | Mark Fiers | 31 October 2011, 18:46:29 UTC | preliminary works with new data structure | 31 October 2011, 18:46:29 UTC |
| d446b1b | Mark Fiers | 31 October 2011, 09:41:24 UTC | hagfish_coverage_combine now works with the new data structure | 31 October 2011, 09:41:24 UTC |
| 9710909 | Mark Fiers | 31 October 2011, 08:51:38 UTC | merged / and cleaning hagfish_extract / no more binning! | 31 October 2011, 08:51:38 UTC |
| dbdad71 | Mark Fiers | 31 October 2011, 01:47:47 UTC | generate report | 31 October 2011, 01:47:47 UTC |
| 90ab35f | Mark Fiers | 07 September 2011, 23:55:21 UTC | bugfixes | 07 September 2011, 23:55:21 UTC |
| b89b94f | Mark Fiers | 25 May 2011, 22:28:56 UTC | Merge branch 'master' of 10.38.8.118:/home/mf/project/hagfish * 'master' of 10.38.8.118:/home/mf/project/hagfish: Major bug fix - depended too much on order of a samtools file - did not work with properly sorted files Now outputs combined sets, even if there are no validly aligning pairs Inital commit - generates plots that summarize the coverage distribution | 25 May 2011, 22:28:56 UTC |
| 6381b4f | Mark Fiers | 25 May 2011, 22:28:53 UTC | ongoing work | 25 May 2011, 22:28:53 UTC |
| 0238df2 | Mark Fiers | 25 May 2011, 21:46:14 UTC | Merge branch 'master' of pgenome.crop.cri.nz:/opt/hagfish | 25 May 2011, 21:46:14 UTC |
| f36cb81 | Mark Fiers | 21 May 2011, 09:31:27 UTC | Major bug fix - depended too much on order of a samtools file - did not work with properly sorted files | 21 May 2011, 09:31:27 UTC |
| bbc1fc5 | Mark Fiers | 19 May 2011, 21:48:37 UTC | Now outputs combined sets, even if there are no validly aligning pairs | 19 May 2011, 21:48:37 UTC |
| 6718ac2 | Mark Fiers | 19 May 2011, 11:41:20 UTC | Inital commit - generates plots that summarize the coverage distribution | 19 May 2011, 11:41:20 UTC |
| 3cccee9 | Mark Fiers | 15 December 2010, 01:14:29 UTC | ongoing | 15 December 2010, 01:14:29 UTC |
| d60aeab | Mark Fiers | 15 December 2010, 01:10:52 UTC | ongoing | 15 December 2010, 01:10:52 UTC |
