| c4e046e | Fabien Campagne | 20 June 2016, 15:44:12 UTC | Apply scalability fixes for RealignmentProcessor from parquet protobuf branch onto stable. See changes.txt for details. | 20 June 2016, 15:44:12 UTC |
| 7d0866d | Fabien Campagne | 17 November 2015, 20:29:56 UTC | Prevent NPE when id is null. | 17 November 2015, 20:30:48 UTC |
| d7ad548 | Fabien Campagne | 02 March 2015, 20:29:49 UTC | Update change log. | 17 November 2015, 20:30:48 UTC |
| c854a6d | Fabien Campagne | 02 March 2015, 20:25:32 UTC | Remove some stdout debug statements. | 17 November 2015, 20:30:48 UTC |
| ad521db | Fabien Campagne | 02 March 2015, 20:23:12 UTC | Add new mode to infer sex from exome data. Only works for human data. | 17 November 2015, 20:30:48 UTC |
| d828e2d | Fabien Campagne | 26 February 2015, 22:33:53 UTC | Fix problem where end of slice could be after beginning of a following slice. Root cause of bug when processing GobyWeb tag CXKLGJG. | 17 November 2015, 20:30:48 UTC |
| b7eb478 | Fabien Campagne | 22 August 2015, 21:53:25 UTC | Optimizations for large number of reference sequences (>100,000). | 22 August 2015, 21:53:25 UTC |
| 6ed9a59 | Fabien Campagne | 26 November 2014, 17:15:21 UTC | Patch to too many log statements when the alignment does not contain quality scores: Prevent AbstractAlignmentToCompactMode to print more than 10 warnings if quality scores are not available in an alignment. | 26 November 2014, 17:15:21 UTC |
| e28936e | Fabien Campagne | 29 August 2014, 14:26:29 UTC | Update CHANGES and version number for 2.3.4.1 release. | 29 August 2014, 14:26:29 UTC |
| 16d81d0 | Fabien Campagne | 28 August 2014, 19:22:01 UTC | Improve javadoc. | 28 August 2014, 19:22:01 UTC |
| be519a7 | Fabien Campagne | 28 August 2014, 19:21:45 UTC | Fix a bug that caused some slices to occur within annotations, despite the --annotation option being given on the command line. The problem was that the chromosome index was not obtained from the genome and was set to zero, always. | 28 August 2014, 19:21:45 UTC |
| 12dac13 | Fabien Campagne | 19 August 2014, 18:19:05 UTC | Allow lenient import mode for TSV files. This makes it possible to convert TSV files to lucene.index when they have been created with Goby in the past with a \t character as last character of the column line. | 19 August 2014, 18:19:05 UTC |
| 23b49fa | Fabien Campagne | 20 June 2014, 20:59:26 UTC | Close streams after reading header and index | 20 June 2014, 20:59:30 UTC |
| 202efd3 | Fabien Campagne | 20 June 2014, 18:11:20 UTC | Close streams after reading header and index | 20 June 2014, 18:11:20 UTC |
| 4598444 | Fabien Campagne | 04 June 2014, 15:28:32 UTC | Add an option to the fasta-to-compact mode that will convert a set of files and concatenate the result to a single compact-reads file (see new --concat option). | 04 June 2014, 15:28:32 UTC |
| 73f6676 | Fabien Campagne | 30 May 2014, 19:37:32 UTC | Expose version number as a property and provide script to deploy or install Goby jar files to Maven | 30 May 2014, 19:37:32 UTC |
| c315366 | Fabien Campagne | 09 May 2014, 20:20:02 UTC | Restore STRICT_SOMATIC filter. | 09 May 2014, 20:20:32 UTC |
| 1b105c9 | Fabien Campagne | 08 May 2014, 21:13:06 UTC | Removed a little too much in the last commit. | 08 May 2014, 21:44:36 UTC |
| 85b4cfd | Fabien Campagne | 08 May 2014, 17:53:47 UTC | Remove dependency on R connection for somatic variation output. This change removes the p-value field. | 08 May 2014, 17:53:47 UTC |
| 3a7cf0f | Fabien Campagne | 08 May 2014, 15:39:40 UTC | Add a mode to test that the connection from Goby to R is working (requires JRI and R built with shared library support). The mode is called test-r-connection (tcr). | 08 May 2014, 15:42:27 UTC |
| 73c4b06 | Fabien Campagne | 01 May 2014, 21:34:28 UTC | Increase version number to 2.3.4 | 01 May 2014, 21:34:28 UTC |
| df63196 | Fabien Campagne | 01 May 2014, 17:24:06 UTC | Activate import of quality scores in last-to-compact mode. | 01 May 2014, 17:24:06 UTC |
| 3bc6dc9 | Fabien Campagne | 01 May 2014, 17:21:06 UTC | Extend LastParser to parse quality scores (assumes alignment was done with -Q1 with scores on the Phred scale). | 01 May 2014, 17:21:06 UTC |
| 00f5df8 | Fabien Campagne | 30 April 2014, 22:47:02 UTC | LastToCompact mode now supports the import of paired end alignments produced by last-pair-probs.sh. | 30 April 2014, 22:47:02 UTC |
| fae85bd | Fabien Campagne | 28 April 2014, 16:44:03 UTC | Synchronize the object sets used in parallel. | 28 April 2014, 17:11:13 UTC |
| 9302285 | Fabien Campagne | 28 April 2014, 16:41:11 UTC | Upgrade to the latest version of the fastutil library. | 28 April 2014, 16:43:38 UTC |
| 511fee7 | Fabien Campagne | 03 April 2014, 17:42:24 UTC | Expose the default sub-sample size with a dynamic option called sub-sample-size in IterateSortedAlignmentsListImpl. (-x IterateSortedAlignmentsListImpl:sub-sample-size <int>) | 03 April 2014, 17:42:24 UTC |
| 3182b43 | Fabien Campagne | 02 April 2014, 21:44:23 UTC | Add a timeout for waiting on other threads. | 02 April 2014, 21:44:23 UTC |
| df3853f | Fabien Campagne | 02 April 2014, 20:10:49 UTC | reads-file-stats: remove any path from basename in the output. | 02 April 2014, 20:10:49 UTC |
| bfc879d | Fabien Campagne | 02 April 2014, 17:47:17 UTC | Close the scanning outputStream when we are done with it and propagate the message that the thread is done. | 02 April 2014, 17:54:01 UTC |
| bc1b950 | Fabien Campagne | 02 April 2014, 16:21:33 UTC | Merge branch 'stable' of https://github.com/CampagneLaboratory/goby into stable | 02 April 2014, 16:21:33 UTC |
| 01b15a6 | Fabien Campagne | 02 April 2014, 16:14:04 UTC | One last optimization. This version now has constant speed irrespective of the time it has been running. | 02 April 2014, 16:14:04 UTC |
| 67a6e29 | Fabien Campagne | 02 April 2014, 16:01:17 UTC | Add two methods to AlignmentReader to determine the minimum and maximum genomic locations represented in the reader. This is useful when suggesting slices to split a set of alignments. This commit includes a fix for possible null start or end positions in slices generated with suggest-position-slices. | 02 April 2014, 16:01:17 UTC |
| 4dfe452 | Fabien Campagne | 02 April 2014, 15:56:33 UTC | Optimize the speed of genotyping when some sites have very high coverage (>500M bases). Now sub-sampling to keep a random set of 10,000 bases for such sites. | 02 April 2014, 15:56:33 UTC |
| 416dabf | Fabien Campagne | 10 February 2014, 21:42:28 UTC | Adjust checkout message to take into account the removal of the submodules | 10 February 2014, 21:42:28 UTC |
| c39a708 | Fabien Campagne | 10 February 2014, 21:41:22 UTC | Merge branch 'stable' of bitbucket.org:campagnelaboratory/goby into stable | 10 February 2014, 21:41:22 UTC |
| e059a5c | Fabien Campagne | 10 February 2014, 19:32:39 UTC | Remove submodules for buildsupport and testsupport. Instead, add buildsupport and testsupport source tree directly. Should make it easier for others to build the project. | 10 February 2014, 21:17:28 UTC |
| 388882e | Fabien Campagne | 20 December 2013, 20:49:34 UTC | Make sure strand bias filter removes up to the last base with strand bias, even if that base means going below the jPlusOne threshold in that sample. | 20 December 2013, 20:54:31 UTC |
| 321adb7 | Fabien Campagne | 20 December 2013, 20:26:06 UTC | Test was incorrectly filtering twice (problem introduced when working on strands filter feature). | 20 December 2013, 20:26:06 UTC |
| c8931df | Fabien Campagne | 20 December 2013, 19:07:59 UTC | Adjust to change in semantic of contains method. | 20 December 2013, 19:07:59 UTC |
| 57d62af | Fabien Campagne | 20 December 2013, 19:07:43 UTC | Adjust expected test output for new FILTER field. | 20 December 2013, 19:07:43 UTC |
| 56f791c | Fabien Campagne | 19 December 2013, 22:39:25 UTC | Improve changelog descriptions. | 19 December 2013, 22:39:25 UTC |
| 15013de | Fabien Campagne | 19 December 2013, 22:24:43 UTC | Add enough germline bases that the coverage filter does not remove the somatic variation. | 19 December 2013, 22:24:43 UTC |
| 4954564 | Fabien Campagne | 19 December 2013, 22:02:34 UTC | Fix syntax errors. | 19 December 2013, 22:02:34 UTC |
| ef1ca75 | Fabien Campagne | 19 December 2013, 22:00:28 UTC | Merge branch 'stable' of github.com:CampagneLaboratory/goby into stable Conflicts: src/edu/cornell/med/icb/goby/alignments/SomaticVariationOutputFormat.java | 19 December 2013, 22:00:28 UTC |
| c5ad8e3 | Fabien Campagne | 19 December 2013, 15:04:15 UTC | Merge strands branch into stable. | 19 December 2013, 15:04:15 UTC |
| 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 |
| 96a1aac | Fabien Campagne | 16 December 2013, 20:50:27 UTC | Remove candidate somatic variation that can occur when the germline samples have less coverage than the somatic sample. Now require at least twice the coverage in the somatic sample than the minimum coverage in the germline samples. | 16 December 2013, 20:50:27 UTC |
| b801b54 | Fabien Campagne | 08 November 2013, 17:17:05 UTC | Remove debugging code. | 08 November 2013, 17:17:05 UTC |
| a28c655 | Fabien Campagne | 08 November 2013, 17:07:52 UTC | Change priority variable calculation to use float rather than double. Do not divide by zero if they are no parents or germline samples. | 08 November 2013, 17:07:52 UTC |
| e99826d | Fabien Campagne | 08 November 2013, 16:10:35 UTC | Change priority variable calculation to use float rather than double. | 08 November 2013, 16:10:35 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 |
| 54de8be | Fabien Campagne | 01 November 2013, 21:41:47 UTC | Add debug assert from stable branch. | 01 November 2013, 21:41:47 UTC |
| 3780b4f | Fabien Campagne | 01 November 2013, 21:17:17 UTC | Add debug assert from stable branch. | 01 November 2013, 21:24:05 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 |
