| c1f4795 | Fabien Campagne | 17 December 2013, 23:08:38 UTC | Replace Double.MIN_VALUE with -10. JSON does not like very small double values and they prevent the table from showing in GobyWeb. | 17 December 2013, 23:08:38 UTC |
| 257bc3c | Fabien Campagne | 17 December 2013, 21:52:53 UTC | Describe latest changes. | 17 December 2013, 21:52:53 UTC |
| e265ccf | Fabien Campagne | 17 December 2013, 21:29:38 UTC | Fix FDR mode to prevent NPE when a FILTER column is specified. | 17 December 2013, 21:29:38 UTC |
| caf7db1 | Fabien Campagne | 17 December 2013, 21:02:21 UTC | Fix the calculation of STRICT_SOMATIC filter and the normalization of the priority score. | 17 December 2013, 21:02:21 UTC |
| 42316a5 | Fabien Campagne | 17 December 2013, 17:45:58 UTC | Add a STRICT_SOMATIC filter. | 17 December 2013, 17:45:58 UTC |
| 63cb7ec | Fabien Campagne | 17 December 2013, 16:46:00 UTC | Take the max or normalized priority contributions rather than the average. | 17 December 2013, 16:46:00 UTC |
| 1cf1ccb | Fabien Campagne | 17 December 2013, 16:17:45 UTC | Improve implementation of SampleCountInfo.baseString. Add method to explain the candidate somatic choices. | 17 December 2013, 16:17:45 UTC |
| 539e0bf | Fabien Campagne | 16 December 2013, 20:50:27 UTC | Fix how parentHasGenotype is calculated. Need to consider the bases remaining after failed bases as well. | 17 December 2013, 16:14:14 UTC |
| eb44c1d | Fabien Campagne | 16 December 2013, 22:13:06 UTC | Avoid NaN when they are no additional germline samples. Use somatic base count in the calculation of priority score. | 16 December 2013, 22:13:06 UTC |
| 427c8e5 | Fabien Campagne | 01 November 2013, 22:46:55 UTC | Fix old test, break new one. The problem is with the test rather than recent changes to the code base. | 01 November 2013, 22:46:55 UTC |
| cc5823f | Fabien Campagne | 01 November 2013, 21:20:57 UTC | Add debug assert from stable branch. | 01 November 2013, 21:20:57 UTC |
| 9086d8d | Fabien Campagne | 01 November 2013, 21:13:15 UTC | Add debug assert. | 01 November 2013, 21:13:15 UTC |
| b365d15 | Fabien Campagne | 01 November 2013, 20:40:40 UTC | Set parameter j to value used when developing the test. | 01 November 2013, 20:40:40 UTC |
| e66c89f | Fabien Campagne | 01 November 2013, 20:35:23 UTC | Make strand bias filter take minimum depth threshold as a parameter (j). | 01 November 2013, 20:35:23 UTC |
| 9535c56 | Fabien Campagne | 01 November 2013, 20:34:42 UTC | Fix for minimum number of reads bug. | 01 November 2013, 20:34:42 UTC |
| 934d22f | Fabien Campagne | 01 November 2013, 19:30:56 UTC | Add strand bias filter. | 01 November 2013, 19:30:56 UTC |
| 346540c | Fabien Campagne | 31 October 2013, 22:44:25 UTC | Adjust Change log. | 31 October 2013, 22:44:25 UTC |
| ac4009a | Fabien Campagne | 31 October 2013, 22:43:48 UTC | Normalize somatic priority score by number of mapped reads, and number of parents and germline samples used in the calculation. | 31 October 2013, 22:43:48 UTC |
| 7ceee9d | Fabien Campagne | 31 October 2013, 19:45:34 UTC | Refactor code base to keep base counts for forward and reverse strands separately in SampleCountInfo. | 31 October 2013, 19:45:34 UTC |
| f9f24bd | Fabien Campagne | 11 October 2013, 22:37:40 UTC | Merge branch 'stable' of bitbucket.org:fac2003/goby into stable Conflicts: CHANGES.txt | 11 October 2013, 22:37:40 UTC |
| 1ff8be0 | Fabien Campagne | 09 October 2013, 15:36:17 UTC | Use a WarningCounter to limit warning to 10 instances. This is needed to avoid writing Gb of log output when the threshold is met. Conflicts: CHANGES.txt | 11 October 2013, 22:36:31 UTC |
| 62eea45 | Fabien Campagne | 07 October 2013, 01:49:04 UTC | Fix condition. Greater or equal is true when zero is on either side. | 07 October 2013, 01:49:04 UTC |
| f597a96 | Fabien Campagne | 07 October 2013, 00:11:45 UTC | Hard limit on parent and germline count. | 07 October 2013, 00:11:45 UTC |
| 387439f | Fabien Campagne | 06 October 2013, 23:21:28 UTC | Simplified isSomaticCandidate method to use frequencies across all types of samples. | 06 October 2013, 23:21:28 UTC |
| c3f81b1 | Fabien Campagne | 06 October 2013, 23:09:17 UTC | Calculate maxPriority only over somatic candidates. | 06 October 2013, 23:09:17 UTC |
| 3817c4c | Fabien Campagne | 06 October 2013, 22:29:13 UTC | Remove filter on (germlineCount > failedCountGermline) because some germline samples may be contaminated by somatic cells and there is no threshold w ecan use to call something not a candidate. Add a priority score that measures the support for a site having a somatic variation. | 06 October 2013, 22:29:13 UTC |
| e957ac1 | Fabien Campagne | 06 October 2013, 16:33:28 UTC | Do not report a somatic candidate when either parent has more than 10 bases supporting the genotype, or the germlines have more than 10. | 06 October 2013, 16:33:28 UTC |
| 7588fab | Fabien Campagne | 05 October 2013, 21:55:24 UTC | Improve description of changes. | 05 October 2013, 21:55:24 UTC |
| 95ad7f3 | Fabien Campagne | 05 October 2013, 21:47:45 UTC | Add unit test to check that issue with homozygous parents, het patient is fixed. | 05 October 2013, 21:47:45 UTC |
| 3133055 | Fabien Campagne | 05 October 2013, 19:55:18 UTC | Fix a couple of bugs and add tests with mockup for somatic variation calls. | 05 October 2013, 19:55:18 UTC |
| a430ca2 | Fabien Campagne | 05 October 2013, 17:41:56 UTC | update test result to reflect introduction of frequency INFO field in somatic format. | 05 October 2013, 17:41:56 UTC |
| b545076 | Fabien Campagne | 04 October 2013, 23:06:58 UTC | Add filters to remove variations that are not somatic, but are prioritized by the p-value when parents are homozygote and the patient is heterozygote. | 04 October 2013, 23:06:58 UTC |
| 74f659b | Fabien Campagne | 04 August 2013, 20:02:25 UTC | Trim mode: remove need for an output filename. Change contains method to remove the smaller bit of sequence flanking the adapter. | 04 August 2013, 20:02:25 UTC |
| 92377b2 | Fabien Campagne | 22 July 2013, 16:23:49 UTC | Adjust CHANGES and version number for 2.3.2 release. | 22 July 2013, 16:23:49 UTC |
| 0209e73 | Fabien Campagne | 19 July 2013, 22:06:10 UTC | run-parallel-mode now supports paired input files. | 19 July 2013, 22:06:10 UTC |
| 86d5cce | Fabien Campagne | 16 July 2013, 14:44:30 UTC | Add --force-quality-encoding option. | 16 July 2013, 14:44:30 UTC |
| 915f63b | Fabien Campagne | 15 July 2013, 21:37:01 UTC | Switch to non-static builder method. | 15 July 2013, 21:37:01 UTC |
| be97ef3 | Fabien Campagne | 15 July 2013, 17:31:38 UTC | suggest-position-slices: fix problem where first slice of genome was omitted from output (with new split by number of bytes option introduced in 2.3). | 15 July 2013, 17:31:38 UTC |
| 4e6be5f | Fabien Campagne | 02 July 2013, 16:15:50 UTC | Prepare for release version 2.3.1 | 02 July 2013, 16:15:50 UTC |
| 172a4cf | Fabien Campagne | 02 July 2013, 15:49:07 UTC | Do not use the static method, it seems that it keeps data around in the class, which degrades performance sharply when processing tens of millions of reads with the same reader. This fixes a tricky performance bug. | 02 July 2013, 15:57:59 UTC |
| f93a834 | Fabien Campagne | 28 June 2013, 21:50:18 UTC | DistinctValueCounterBitSet: now grows to biggest size at construction time. | 28 June 2013, 21:50:18 UTC |
| 50f2d95 | Fabien Campagne | 28 June 2013, 21:39:34 UTC | Fix suggest-position-slices (end of chromosome too long by one base). | 28 June 2013, 21:41:48 UTC |
| b260542 | Fabien Campagne | 10 June 2013, 14:32:52 UTC | Describe fix in changelog. | 10 June 2013, 14:32:52 UTC |
| 65f8a50 | Fabien Campagne | 09 June 2013, 15:06:55 UTC | Fix for GitHub Goby issue 3. | 09 June 2013, 15:08:19 UTC |
| d584c49 | Fabien Campagne | 26 April 2013, 14:47:42 UTC | Update version numbers, prepare for 2.3 release. | 26 April 2013, 14:47:42 UTC |
| 55a02ca | Fabien Campagne | 26 April 2013, 14:44:47 UTC | Adding vcf files with different headers. May be used to test fdr mode with different headers at some later point. | 26 April 2013, 14:44:47 UTC |
| 3fdfef2 | Fabien Campagne | 19 April 2013, 18:21:55 UTC | Add verbose flag for trim mode. | 19 April 2013, 18:21:55 UTC |
| 4660e6b | Fabien Campagne | 18 April 2013, 20:01:23 UTC | Improve trim mode to store pair read length after trimming, and use trim-left and --trim-right parameters. | 18 April 2013, 20:01:23 UTC |
| 4c7dc11 | Fabien Campagne | 15 April 2013, 19:37:02 UTC | Fix suggest-position-slices (end of chromosome too long by one base). | 15 April 2013, 19:37:02 UTC |
| cb3e663 | Fabien Campagne | 15 April 2013, 19:19:13 UTC | Fix suggest-position-slices (bug would leave out some slices when restrict-with-chromosome was active). | 15 April 2013, 19:19:13 UTC |
| 100c1e7 | Fabien Campagne | 15 April 2013, 16:31:01 UTC | Remove left-over filter for somatic variations. | 15 April 2013, 16:31:01 UTC |
| b9a1720 | Fabien Campagne | 13 April 2013, 21:12:02 UTC | Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices | 13 April 2013, 21:12:02 UTC |
| 6e6ba7e | Fabien Campagne | 13 April 2013, 21:11:22 UTC | Try to avoid java.lang.StringIndexOutOfBoundsException: String index out of range: 12 at java.lang.String.charAt(String.java:687) at edu.cornell.med.icb.goby.alignments.ExportableAlignmentEntryData.buildFrom(ExportableAlignmentEntryData.java:582) | 13 April 2013, 21:11:22 UTC |
| c5c9706 | Fabien Campagne | 13 April 2013, 20:56:53 UTC | Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices | 13 April 2013, 20:56:53 UTC |
| 33c9b30 | Fabien Campagne | 13 April 2013, 20:55:31 UTC | Add some debug methods. | 13 April 2013, 20:55:31 UTC |
| 86ce532 | Fabien Campagne | 13 April 2013, 20:52:14 UTC | Try to avoid java.lang.StringIndexOutOfBoundsException: String index out of range: 12 at java.lang.String.charAt(String.java:687) at edu.cornell.med.icb.goby.alignments.ExportableAlignmentEntryData.buildFrom(ExportableAlignmentEntryData.java:582) | 13 April 2013, 20:52:14 UTC |
| 38715f1 | Fabien Campagne | 13 April 2013, 17:13:22 UTC | Fix artifact id. | 13 April 2013, 17:13:22 UTC |
| 3193093 | Fabien Campagne | 13 April 2013, 17:01:26 UTC | Update version numbers for 2.3 SNAPSHOT. | 13 April 2013, 17:01:26 UTC |
| b943254 | Fabien Campagne | 13 April 2013, 16:59:40 UTC | Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices | 13 April 2013, 16:59:40 UTC |
| 655cf06 | Fabien Campagne | 13 April 2013, 16:58:21 UTC | Add field to store chromosome index. | 13 April 2013, 16:58:21 UTC |
| 9fcfc79 | Fabien Campagne | 11 April 2013, 20:59:31 UTC | suggest-position-slices: Add --restrict-per-chromosome option. When this switch is provided, slices will be restricted to start and end on the same chromosome. This is useful to produce intervals to give Mutect, for instance. | 11 April 2013, 20:59:31 UTC |
| 98fe12a | Fabien Campagne | 11 April 2013, 18:57:29 UTC | Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices | 11 April 2013, 18:57:29 UTC |
| d8a4e1c | Fabien Campagne | 11 April 2013, 18:54:08 UTC | Add Mutect format test. No dash required. | 11 April 2013, 18:54:08 UTC |
| a901cc4 | Fabien Campagne | 11 April 2013, 16:59:53 UTC | Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices | 11 April 2013, 16:59:53 UTC |
| 6652a4e | Fabien Campagne | 11 April 2013, 16:59:09 UTC | Avoid possible java.lang.NegativeArraySizeException, when a meta comment does not include an equal sign (## muTector v1.0.47986) | 11 April 2013, 16:59:09 UTC |
| 0ee229d | Fabien Campagne | 11 April 2013, 03:27:26 UTC | Fix NPE when a genomic slice is not provided. | 11 April 2013, 03:27:26 UTC |
| 7c12d35 | Fabien Campagne | 09 April 2013, 17:38:02 UTC | Fix possible out of ArrayIndexOutOfBoundsException. | 10 April 2013, 13:53:02 UTC |
| 3953a7c | Fabien Campagne | 09 April 2013, 16:49:34 UTC | Fix possible out of ArrayIndexOutOfBoundsException. | 09 April 2013, 16:49:34 UTC |
| 36d2bb8 | Fabien Campagne | 04 April 2013, 21:06:09 UTC | Add random guards to QualityScoreFilter. Random guards prevent discarding all bases for a genotype if this genotype represents a major fraction of bases observed at a site. This avoids false negatives where genotypes could be discarded because quality was too low for all supporting bases, even though most bases had the same genotype. Behavior compatible with Goby 2.2.1- can be restored with a dynamic option, see option NoRandomGuard in QualityScoreFilter. | 04 April 2013, 21:06:09 UTC |
| f649617 | Fabien Campagne | 04 April 2013, 21:03:15 UTC | Improvements to goby shell script: remove quotes from variable when setting RJAVA_HOME and better code to find goby jar file (Thanks Manuele Simi for the WORKING_DIR solution). | 04 April 2013, 21:03:15 UTC |
| 968f0e1 | Fabien Campagne | 03 April 2013, 21:41:53 UTC | Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices | 03 April 2013, 21:41:53 UTC |
| 71247ee | Fabien Campagne | 03 April 2013, 21:35:02 UTC | concatenate-alignments mode: Add a mechanism to override/define read groups/read origin info on the fly when reading alignments that did not include them. Coupled with changes to compact-to-sam, this makes it possible to get BAM files with read groups directly from Goby alignments. | 03 April 2013, 21:39:18 UTC |
| 80173fd | Fabien Campagne | 03 April 2013, 21:35:02 UTC | concatenate-alignments mode: Add a mechanism to override/define read groups/read origin info on the fly when reading alignments that did not include them. Coupled with changes to compact-to-sam, this makes it possible to get BAM files with read groups directly from Goby alignments. | 03 April 2013, 21:35:02 UTC |
| 9439915 | Fabien Campagne | 03 April 2013, 21:32:35 UTC | compact-to-sam mode: fixed writting of read groups, which were not correctly written for platform, platform unit, and library. | 03 April 2013, 21:32:35 UTC |
| 5c05a0f | Fabien Campagne | 03 April 2013, 18:33:40 UTC | - concatenate-alignments mode: add ability to restrict output to a genomic slice (see -s and -e options). - API change: AlignmentSliceHelper makes it easier to parse and process genomic slices for sets of alignments. - concatenate-alignments mode: now transfers read groups to output in the same way that non-sorted concat does. | 03 April 2013, 18:33:40 UTC |
| 38722d9 | Fabien Campagne | 01 April 2013, 20:55:29 UTC | Fix URL for test data via the web. | 01 April 2013, 20:55:29 UTC |
| 26c4ada | Fabien Campagne | 01 April 2013, 20:02:47 UTC | Update version numbers for release. | 01 April 2013, 20:02:47 UTC |
| 639eca1 | Fabien Campagne | 01 April 2013, 17:38:35 UTC | Adjust changes. | 01 April 2013, 17:38:35 UTC |
| c035efc | Fabien Campagne | 01 April 2013, 17:32:35 UTC | Expose some parameters are dynamic options. Keep track of candidates screened in new filters. | 01 April 2013, 17:32:35 UTC |
| cb6f652 | Fabien Campagne | 31 March 2013, 16:51:45 UTC | Fix possible NPE. | 31 March 2013, 16:51:45 UTC |
| 1301c7b | Fabien Campagne | 31 March 2013, 15:30:20 UTC | Softer filter to remove candidates when the genotype exists in the germline. | 31 March 2013, 15:32:59 UTC |
| 4062a65 | Fabien Campagne | 30 March 2013, 19:05:57 UTC | Somatic variation output format: do not consider genotypes that are also seen in germline (use 1 base as the cutoff). | 30 March 2013, 19:05:57 UTC |
| 1bf08f6 | Fabien Campagne | 30 March 2013, 16:07:40 UTC | Somatic variation output format: restore left-over filter, but with multiplier=1. | 30 March 2013, 18:43:26 UTC |
| 50c6070 | Fabien Campagne | 30 March 2013, 15:37:57 UTC | more stringent filter on indels, keep indels at site when no more than one indel genotype detected. | 30 March 2013, 15:37:57 UTC |
| d18887a | Fabien Campagne | 29 March 2013, 22:20:27 UTC | Adust junit test results for fdr changes. Resolve bugs caught by junits. | 29 March 2013, 22:20:27 UTC |
| b94a9b2 | Fabien Campagne | 29 March 2013, 21:19:37 UTC | discover-sequence-variants: Add a new filter to remove indels at a site where a sample shows lots of distinct possible indels. Indels at these sites are very likely to be artefactual. We count the number of samples where three distinct indel genotypes are seen. If more than 1/4 of the samples have likely indel artifacts, we remove all indel candidates at the site. This filter is added to the somatic variations output format. | 29 March 2013, 21:19:37 UTC |
| c520c9d | Fabien Campagne | 29 March 2013, 19:33:40 UTC | - discover-sequence-variants: remove left-over filter for somatic variations output format. | 29 March 2013, 19:33:40 UTC |
| c8a5099 | Fabien Campagne | 29 March 2013, 19:32:08 UTC | - compact-file-stats mode: print progress when scanning reads files. Use a buffered reader to improve read file parsing performance. | 29 March 2013, 19:32:08 UTC |
| da7c9ae | Fabien Campagne | 29 March 2013, 18:54:21 UTC | discover-sequence-variants mode: add assertion to give hint to user that syntax is incorrect in for -s and -e options. | 29 March 2013, 18:54:53 UTC |
| fcea09b | Fabien Campagne | 29 March 2013, 15:31:49 UTC | - discover-sequence-variants mode: list somatic_variations output format in help. | 29 March 2013, 15:31:49 UTC |
| 08b35da | Fabien Campagne | 29 March 2013, 15:19:23 UTC | discover-sequence-variation mode: name the items, they are aligned reads, not genomic positions. | 29 March 2013, 15:19:23 UTC |
| 7646c2e | Fabien Campagne | 29 March 2013, 15:18:20 UTC | - Somatic variation output format: fix silly bug that produced false negative p-values when all somatic samples did not have the variation. The bug did not affect comparisons where only one somatic/germline pair was considered. | 29 March 2013, 15:18:20 UTC |
| 8ceeeb7 | Fabien Campagne | 28 March 2013, 17:46:42 UTC | - Somatic variation output format: handle unrecognized sample-ids in the parents column. | 28 March 2013, 17:46:42 UTC |
| 3fbc905 | Fabien Campagne | 20 March 2013, 18:45:15 UTC | - FDR mode: add ability to read groups from VCF file and adjust columns/fields marked as p-value. Mark adjusted columns with group q-value. - Somatic variation output format: annotate somatic p-value column with 'p-value' group. Fix the type of the p-value column to be a number (was String in release 2.2). | 20 March 2013, 18:45:15 UTC |
| 7cc0621 | Fabien Campagne | 19 March 2013, 20:53:34 UTC | updated version numbers for python and c++ APIs | 19 March 2013, 20:53:34 UTC |
| f1bce40 | Fabien Campagne | 19 March 2013, 20:50:07 UTC | prepare for 2.2 release | 19 March 2013, 20:50:07 UTC |
| cc1bc27 | Fabien Campagne | 19 March 2013, 19:37:06 UTC | Merge branch 'locations-by-bytes' into somatic | 19 March 2013, 19:37:06 UTC |
| c912262 | Fabien Campagne | 19 March 2013, 19:31:50 UTC | Mode suggest-position-slices: add option number-of-bytes to suggest slices with a uniform number of compressed bytes. This option aims to provide more balanced slices in bases where the genome as very non uniform coverage by position. With this option, the number of slices is determined to yield slices that need to decompress about the amount of bytes indicated on the command line. | 19 March 2013, 19:31:50 UTC |
| c45da25 | Fabien Campagne | 19 March 2013, 17:01:00 UTC | Fix thresholding effect for indels. | 19 March 2013, 17:01:00 UTC |
| b13330e | Fabien Campagne | 18 March 2013, 18:40:25 UTC | Fix expected indel frequency model. When reverting indel counts to avoid thresholding effect, remove indel from failed indel list. | 18 March 2013, 18:40:25 UTC |
