| 3b56974 | David A. Parry | 10 July 2020, 10:56:40 UTC | Update readme.md | 10 July 2020, 10:56:40 UTC |
| 2bcf574 | David A. Parry | 27 February 2019, 22:01:15 UTC | fix ref dependant X chromosome | 27 February 2019, 22:01:15 UTC |
| d631cca | David A. Parry | 18 January 2019, 14:20:13 UTC | bug fixes | 18 January 2019, 14:20:13 UTC |
| a9c7e68 | David A. Parry | 22 June 2018, 08:35:23 UTC | formatting | 22 June 2018, 08:35:23 UTC |
| 73a9c5f | David A. Parry | 14 June 2018, 13:59:35 UTC | check iterator is defined before calling next | 14 June 2018, 13:59:35 UTC |
| 907a285 | David A. Parry | 14 June 2018, 13:58:46 UTC | CSQ fields should be lowercase | 14 June 2018, 13:58:46 UTC |
| 94381a3 | David A. Parry | 06 April 2018, 10:46:07 UTC | support use of coordinates as well as genes | 06 April 2018, 10:46:07 UTC |
| b90c152 | David A. Parry | 06 April 2018, 10:45:16 UTC | support (b)gzip compressed VCFs | 06 April 2018, 10:45:16 UTC |
| 623816c | David A. Parry | 06 April 2018, 10:44:50 UTC | update submodule with REST query fix | 06 April 2018, 10:44:50 UTC |
| af931ca | David A. Parry | 16 March 2018, 16:40:38 UTC | submodule update | 16 March 2018, 16:40:38 UTC |
| 0d21ad7 | David A. Parry | 16 March 2018, 13:52:51 UTC | add geneAnnotatorDb.zip link | 16 March 2018, 13:52:51 UTC |
| 595c882 | David A. Parry | 16 March 2018, 13:46:43 UTC | submodule update | 16 March 2018, 13:46:43 UTC |
| 4483b86 | David A. Parry | 06 March 2018, 10:46:40 UTC | remove Sys::CPU dependency | 06 March 2018, 10:46:40 UTC |
| 2615280 | David A. Parry | 23 February 2018, 15:52:00 UTC | fix getContigOrder calls | 23 February 2018, 15:52:00 UTC |
| 0497024 | David A. Parry | 02 November 2017, 15:02:56 UTC | fix next statements which should be returns | 02 November 2017, 15:02:56 UTC |
| 4b04817 | David A. Parry | 16 August 2017, 09:25:17 UTC | attempt better standardisation of INFO/WARN messages | 16 August 2017, 09:25:17 UTC |
| 966fcbc | David A. Parry | 15 August 2017, 15:50:20 UTC | message formatting | 15 August 2017, 15:50:20 UTC |
| aff5c36 | David A. Parry | 15 August 2017, 15:31:21 UTC | progress fixes | 15 August 2017, 15:31:21 UTC |
| eb00bdb | David A. Parry | 15 August 2017, 15:14:11 UTC | remove redundant variant count | 15 August 2017, 15:14:11 UTC |
| dbab041 | David A. Parry | 15 August 2017, 15:08:38 UTC | getProgressBar should return count of variants from file | 15 August 2017, 15:08:38 UTC |
| 3e88360 | David A. Parry | 14 August 2017, 16:06:03 UTC | add VcfReader fixes for contig names containing colons. | 14 August 2017, 16:06:03 UTC |
| 3863678 | David A. Parry | 14 August 2017, 15:56:12 UTC | Merge branch 'master' of https://github.com/gantzgraf/vcfhacks | 14 August 2017, 15:56:12 UTC |
| a3b3500 | David A. Parry | 14 August 2017, 15:55:54 UTC | ensure we only retrieve one variant where we have a neighbouring SNP | 14 August 2017, 15:55:54 UTC |
| 668cfdc | David A. Parry | 14 June 2017, 10:52:40 UTC | handle annotations with gene symbols instead of IDs | 14 June 2017, 10:52:40 UTC |
| c7bfbd8 | David A. Parry | 01 June 2017, 14:47:00 UTC | update submodule | 01 June 2017, 14:47:00 UTC |
| 930ab7b | David A. Parry | 26 May 2017, 14:25:58 UTC | add start_lost variant | 26 May 2017, 14:25:58 UTC |
| 8338bda | David A. Parry | 26 May 2017, 14:16:39 UTC | add non_coding_transcript_exon_variant and non_coding_transcript_variant | 26 May 2017, 14:16:39 UTC |
| 6207073 | David A. Parry | 26 May 2017, 14:16:03 UTC | allow to work on piped data | 26 May 2017, 14:16:03 UTC |
| 9d60cec | David A. Parry | 26 May 2017, 14:09:27 UTC | correct more heading formatting | 26 May 2017, 14:09:27 UTC |
| 4f10256 | David A. Parry | 26 May 2017, 14:08:00 UTC | correct heading formatting | 26 May 2017, 14:08:00 UTC |
| 39b7d97 | David A. Parry | 17 May 2017, 09:37:44 UTC | update submodule with sortVcf fixes | 17 May 2017, 09:37:44 UTC |
| d8d3e57 | David A. Parry | 12 May 2017, 15:23:31 UTC | add -v/--add_variant_classes option | 12 May 2017, 15:23:31 UTC |
| 75ef943 | David A. Parry | 02 May 2017, 11:20:02 UTC | update submodule with _replaceHeaderContigs fix | 02 May 2017, 11:20:02 UTC |
| f183f60 | David A. Parry | 02 May 2017, 11:12:37 UTC | Update submodule with sortVcf fix | 02 May 2017, 11:12:37 UTC |
| 984f4bc | David A. Parry | 02 May 2017, 11:11:44 UTC | fix error in find shared genes min matching samples | 02 May 2017, 11:11:44 UTC |
| 8f7df79 | David A. Parry | 28 April 2017, 13:31:37 UTC | Merge branch 'master' of https://github.com/gantzgraf/vcfhacks | 28 April 2017, 13:31:37 UTC |
| 320adba | David A. Parry | 28 April 2017, 13:31:18 UTC | Merge branch 'master' of https://github.com/gantzgraf/vcfhacks | 28 April 2017, 13:31:18 UTC |
| d03eaee | David A. Parry | 28 April 2017, 13:31:06 UTC | use gnomAD POPMAX annotation | 28 April 2017, 13:31:06 UTC |
| 5a4cec9 | David A. Parry | 27 April 2017, 13:22:00 UTC | update to use new VcfReader getContigOrder args | 27 April 2017, 13:22:00 UTC |
| b5082f5 | David A. Parry | 27 April 2017, 13:21:58 UTC | update submodule with sortVcf function that works on streams | 27 April 2017, 13:21:58 UTC |
| 6de96b2 | David A. Parry | 26 April 2017, 22:22:18 UTC | update submodule | 26 April 2017, 22:22:18 UTC |
| d229d4a | David A. Parry | 26 April 2017, 12:10:44 UTC | Merge branch 'master' of https://github.com/gantzgraf/vcfhacks | 26 April 2017, 12:10:44 UTC |
| 12cbdcc | David A. Parry | 26 April 2017, 12:09:57 UTC | update submodule | 26 April 2017, 12:09:57 UTC |
| 14849be | David A. Parry | 25 April 2017, 10:01:36 UTC | move to accessories | 25 April 2017, 10:01:36 UTC |
| a2bbc91 | David A. Parry | 25 April 2017, 10:01:13 UTC | correct example options | 25 April 2017, 10:01:13 UTC |
| 37c0499 | David A. Parry | 25 April 2017, 08:40:30 UTC | remove unnecessary import | 25 April 2017, 08:40:30 UTC |
| e066b53 | David A. Parry | 24 April 2017, 15:38:46 UTC | formatting | 24 April 2017, 15:38:46 UTC |
| 3fcb65c | David A. Parry | 24 April 2017, 15:14:33 UTC | fix -u regression | 24 April 2017, 15:14:33 UTC |
| 0c5e6a7 | David A. Parry | 24 April 2017, 14:28:12 UTC | update simpleProgress call | 24 April 2017, 14:28:12 UTC |
| d4f4eaf | David A. Parry | 24 April 2017, 14:27:25 UTC | allow granular simple progress reporting | 24 April 2017, 14:27:25 UTC |
| e473bb1 | gantzgraf | 20 April 2017, 16:33:20 UTC | Merge branch 'master' of https://github.com/gantzgraf/vcfhacks | 20 April 2017, 16:33:20 UTC |
| ad0434f | gantzgraf | 20 April 2017, 16:33:16 UTC | add List::MoreUtils module | 20 April 2017, 16:33:16 UTC |
| a9427be | gantzgraf | 20 April 2017, 16:33:01 UTC | grammar | 20 April 2017, 16:33:01 UTC |
| 74d7a67 | David A. Parry | 14 April 2017, 10:24:32 UTC | warn if using --consensus_splice_site with snpeff mode | 14 April 2017, 10:24:32 UTC |
| 5f6aeb8 | David A. Parry | 14 April 2017, 10:23:47 UTC | update in silico doc, warn on missing dbNSFP fields | 14 April 2017, 10:23:47 UTC |
| 2cfbdca | David A. Parry | 14 April 2017, 10:07:48 UTC | warn if specified dbNSFP field is missing from INFO headers | 14 April 2017, 10:07:48 UTC |
| bceddaa | David A. Parry | 13 April 2017, 14:06:24 UTC | update HTS module version and add Statistics::R module | 13 April 2017, 14:06:24 UTC |
| 01f8ecf | David A. Parry | 13 April 2017, 14:06:06 UTC | add required module | 13 April 2017, 14:06:06 UTC |
| 0d6dfac | David A. Parry | 13 April 2017, 13:33:04 UTC | add explicit test for opening compressed VCF | 13 April 2017, 13:33:04 UTC |
| 1cd559c | David A. Parry | 13 April 2017, 13:29:46 UTC | updated dapPerlGenomicLib submodule | 13 April 2017, 13:29:46 UTC |
| f923ca4 | David A. Parry | 12 April 2017, 14:33:17 UTC | change progress handling to make Term::ProgressBar optional | 12 April 2017, 14:33:17 UTC |
| 1418e61 | David A. Parry | 12 April 2017, 14:32:16 UTC | add generic progress handling functions | 12 April 2017, 14:32:16 UTC |
| 6aab76d | David A. Parry | 11 April 2017, 10:00:31 UTC | update HTS module version | 11 April 2017, 10:00:31 UTC |
| d560de3 | David A. Parry | 07 April 2017, 16:32:47 UTC | add documentation | 07 April 2017, 16:32:47 UTC |
| 50bcb19 | David A. Parry | 07 April 2017, 15:53:34 UTC | improve SnpEff compatibility | 07 April 2017, 15:53:34 UTC |
| afcf64a | David A. Parry | 07 April 2017, 15:53:09 UTC | allow wider range of in silico dbNSFP predictions | 07 April 2017, 15:53:09 UTC |
| 8f4f6cb | David A. Parry | 07 April 2017, 15:52:47 UTC | add note about case-sensitive dbNSFP annotations | 07 April 2017, 15:52:47 UTC |
| 7f0fa7c | David A. Parry | 07 April 2017, 15:50:02 UTC | improve SnpEff in silico prediction support | 07 April 2017, 15:50:02 UTC |
| aeb7820 | David A. Parry | 07 April 2017, 15:49:34 UTC | update --damaging documentation | 07 April 2017, 15:49:34 UTC |
| f4bc33a | David A. Parry | 28 March 2017, 13:03:26 UTC | add option to output individual variant/consequences | 28 March 2017, 13:03:26 UTC |
| f3f0917 | David A. Parry | 28 March 2017, 09:45:27 UTC | change sample allele frequency option to control allele frequency | 28 March 2017, 09:45:27 UTC |
| a692394 | David A. Parry | 27 March 2017, 16:12:29 UTC | add geneBurdenTest.pl script | 27 March 2017, 16:12:29 UTC |
| 0fd832b | David A. Parry | 27 March 2017, 16:11:45 UTC | document --ab option | 27 March 2017, 16:11:45 UTC |
| aa3380f | David A. Parry | 09 March 2017, 10:14:11 UTC | correct error with novel vs Novel variants | 09 March 2017, 10:14:11 UTC |
| 955614b | David A. Parry | 06 March 2017, 13:15:15 UTC | add countVarsPerSample.pl script | 06 March 2017, 13:15:15 UTC |
| 19ce9fe | David A. Parry | 28 February 2017, 15:54:06 UTC | update --score_filter to --eval_filter | 28 February 2017, 15:54:06 UTC |
| 09b36d5 | David A. Parry | 28 February 2017, 12:18:49 UTC | check samples have parents in vcf before doing de novo commands | 28 February 2017, 12:18:49 UTC |
| 7f180f0 | David A. Parry | 28 February 2017, 12:15:32 UTC | fix parent checks for de novos | 28 February 2017, 12:15:32 UTC |
| 0690a0f | David A. Parry | 28 February 2017, 12:07:32 UTC | check samples have parents in vcf before doing de novo commands | 28 February 2017, 12:07:32 UTC |
| 2ea2a57 | David A. Parry | 28 February 2017, 11:03:26 UTC | update ref file locations | 28 February 2017, 11:03:26 UTC |
| 04c46ab | David A. Parry | 07 February 2017, 16:14:51 UTC | update dapPerlGenomicLib with SnpEff header fix | 07 February 2017, 16:14:51 UTC |
| 8fbc363 | David A. Parry | 06 February 2017, 16:06:52 UTC | no longer need to add script location to beginning of commands | 06 February 2017, 16:06:52 UTC |
| 0b56b75 | David A. Parry | 03 February 2017, 10:20:03 UTC | add removeNonMatchingRefs.pl for dealing with 1kg GRCh38 files | 03 February 2017, 10:20:03 UTC |
| 56b84d2 | David A. Parry | 31 January 2017, 12:55:52 UTC | update dapPerlGenomicLib submodule | 31 January 2017, 12:55:52 UTC |
| d547591 | David A. Parry | 06 January 2017, 11:59:32 UTC | remove short -s option for --silent flag | 06 January 2017, 11:59:32 UTC |
| fee0914 | David A. Parry | 05 January 2017, 13:14:44 UTC | correct and alter --species/-s vs --silent flag behaviour | 05 January 2017, 13:14:44 UTC |
| 2e45f31 | David A. Parry | 02 December 2016, 17:04:43 UTC | update submodules | 02 December 2016, 17:04:43 UTC |
| 6c88048 | David A. Parry | 02 December 2016, 17:03:36 UTC | typo | 02 December 2016, 17:03:36 UTC |
| e32b484 | David A. Parry | 02 December 2016, 17:03:19 UTC | allow for non-coding hgvs descriptions | 02 December 2016, 17:03:19 UTC |
| 21df71a | David A. Parry | 08 November 2016, 15:37:59 UTC | update dapPerlGenomicLib | 08 November 2016, 15:37:59 UTC |
| 60d51af | David A. Parry | 08 November 2016, 15:13:58 UTC | add Sort::External and check exit of bioperl install | 08 November 2016, 15:13:58 UTC |
| aab6c8c | David A. Parry | 08 November 2016, 14:31:53 UTC | do bioperl separately | 08 November 2016, 14:31:53 UTC |
| d9ea311 | David A. Parry | 08 November 2016, 14:23:50 UTC | automate as much as possible | 08 November 2016, 14:23:50 UTC |
| 6354b28 | David A. Parry | 08 November 2016, 14:23:32 UTC | add List::MoreUtils to required modules, update testing section | 08 November 2016, 14:23:32 UTC |
| d542050 | David A. Parry | 07 November 2016, 10:31:56 UTC | Merge branch 'install_test' | 07 November 2016, 10:31:56 UTC |
| 1fe0f0b | David A. Parry | 06 November 2016, 12:10:14 UTC | LWP::Protocol::https is required for biogrid download | 06 November 2016, 12:10:14 UTC |
| 1185285 | David A. Parry | 04 November 2016, 16:46:48 UTC | attempt auto config | 04 November 2016, 16:46:48 UTC |
| 5d45af4 | David A. Parry | 04 November 2016, 16:31:03 UTC | use prerequisites_policy | 04 November 2016, 16:31:03 UTC |
| b78d8b7 | David A. Parry | 04 November 2016, 16:18:26 UTC | attempt to install Bio::DB modules using install scripts | 04 November 2016, 16:18:26 UTC |
| fc93bd7 | David A. Parry | 04 November 2016, 15:56:39 UTC | exit with 0 after --help or --man | 04 November 2016, 15:56:39 UTC |
