| a1dd465 | Scott Smith | 05 September 2013, 18:40:13 UTC | remove temp override of GENOME_SW | 05 September 2013, 18:41:18 UTC |
| 1a372ed | Malachi Griffith | 05 September 2013, 18:35:55 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 05 September 2013, 18:35:55 UTC |
| da9d8f2 | Malachi Griffith | 05 September 2013, 18:35:39 UTC | ClinSeq - better warning messages for checking of genotype microarray models | 05 September 2013, 18:35:39 UTC |
| 5cf170b | Feiyu Du | 05 September 2013, 18:33:24 UTC | update blessed build for apipe-test-clinseq-wer | 05 September 2013, 18:33:58 UTC |
| a7f923b | APipe Tester | 05 September 2013, 18:00:09 UTC | Updated `gmt` tab completion. | 05 September 2013, 18:00:09 UTC |
| 61dc0b0 | APipe Tester | 05 September 2013, 17:58:57 UTC | Updated `genome` tab completion. | 05 September 2013, 17:58:57 UTC |
| 4f6a5f9 | APipe Tester | 05 September 2013, 17:56:54 UTC | Updated class browser cache. | 05 September 2013, 17:56:54 UTC |
| c996210 | dmorton | 05 September 2013, 17:47:33 UTC | bugfix: improperly named package code-deduplication: dmorton | 05 September 2013, 17:48:23 UTC |
| ded96e4 | Gabriel Sanderson | 05 September 2013, 17:13:47 UTC | Merge branch 'master' into gb_master | 05 September 2013, 17:13:47 UTC |
| 8077bf7 | Gabriel Sanderson | 05 September 2013, 17:12:47 UTC | Removed unused and duplicate wgs_filter. code-deduplication: mburnett, gsanders | 05 September 2013, 17:12:47 UTC |
| d207bb5 | Mark Burnett | 05 September 2013, 16:52:40 UTC | move print_stats to base class code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:42 UTC |
| 7dc0eed | Mark Burnett | 05 September 2013, 16:41:02 UTC | remove redundant fails_homopolymer_check code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:41 UTC |
| 1b6aec9 | Mark Burnett | 05 September 2013, 16:40:10 UTC | extract _start_position_offset code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:41 UTC |
| 92f3f1e | Mark Burnett | 05 September 2013, 16:39:02 UTC | remove wrong comments code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:40 UTC |
| 17ac438 | Mark Burnett | 05 September 2013, 16:37:00 UTC | rename chr_{start,stop} to {start,stop} code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:39 UTC |
| c8bebc2 | Mark Burnett | 05 September 2013, 16:30:07 UTC | remove redundant read_counts_by_allele code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:39 UTC |
| 42a2fc0 | Mark Burnett | 05 September 2013, 16:27:29 UTC | whitespace | 05 September 2013, 17:08:38 UTC |
| a2e84f5 | Mark Burnett | 05 September 2013, 16:26:43 UTC | remove redundant variant_type code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:38 UTC |
| f6ac9a4 | Mark Burnett | 05 September 2013, 16:26:12 UTC | remove redundant help methods code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:37 UTC |
| ece162b | Mark Burnett | 05 September 2013, 16:25:33 UTC | remove redundant param code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:37 UTC |
| 0895f07 | Mark Burnett | 05 September 2013, 16:24:24 UTC | remove redundant input properties code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:36 UTC |
| 8b5e210 | Mark Burnett | 05 September 2013, 16:23:26 UTC | change base class of G:M:T:DV2:F:FalsePositiveVcfBase code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:36 UTC |
| 9fa2e5c | Mark Burnett | 05 September 2013, 16:17:06 UTC | remove re-declared input properties code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:35 UTC |
| c565648 | Mark Burnett | 05 September 2013, 15:43:18 UTC | change params to inputs code-deduplication: gsanders, mburnett | 05 September 2013, 17:08:35 UTC |
| 1207a85 | Mark Burnett | 05 September 2013, 15:43:06 UTC | whitespace | 05 September 2013, 17:08:34 UTC |
| 6946868 | apregier | 05 September 2013, 16:35:24 UTC | Merge branch 'fix' into gb_master | 05 September 2013, 16:35:24 UTC |
| 733ec91 | apregier | 05 September 2013, 16:16:12 UTC | Non-numeric genotypes are bad. Add a ploidy method | 05 September 2013, 16:25:39 UTC |
| fcd7f8c | apregier | 05 September 2013, 15:50:19 UTC | Changes suggested by Travis | 05 September 2013, 16:25:38 UTC |
| 9bb243c | apregier | 04 September 2013, 20:38:07 UTC | Get a genotype object for a given sample | 05 September 2013, 16:25:37 UTC |
| d2315e9 | apregier | 04 September 2013, 20:17:15 UTC | Genotype object for vcf files | 05 September 2013, 16:25:36 UTC |
| 15af57f | Mark Burnett | 05 September 2013, 16:07:22 UTC | move pod to base code-deduplication: mburnett | 05 September 2013, 16:09:39 UTC |
| 1c825e5 | Feiyu Du | 05 September 2013, 15:33:32 UTC | add .tsv to all terminal dgidb output files | 05 September 2013, 15:34:00 UTC |
| e59363a | Mark Burnett | 05 September 2013, 14:57:09 UTC | BreakdancerMax inherits from Breakdancer code-deduplication: mburnett | 05 September 2013, 15:13:41 UTC |
| 1d83b0c | Mark Burnett | 05 September 2013, 14:51:54 UTC | remove valid_values this restriction doesn't apply to BreakdancerMax code-deduplication: mburnett | 05 September 2013, 15:13:40 UTC |
| 08e6225 | Mark Burnett | 05 September 2013, 14:46:21 UTC | extract _get_chr_list_from_idx_file code-deduplication: mburnett | 05 September 2013, 15:13:40 UTC |
| 09506e0 | Mark Burnett | 05 September 2013, 14:35:57 UTC | use $self->class where appropriate code-deduplication: mburnett | 05 September 2013, 15:13:39 UTC |
| b568502 | Mark Burnett | 05 September 2013, 14:33:11 UTC | extract class_name method this just gets "Breakdancer" or "BreakdancerMax" for use in strings code-deduplication: mburnett | 05 September 2013, 15:13:39 UTC |
| af691f7 | Mark Burnett | 05 September 2013, 14:25:47 UTC | extract chr_list_when_missing_idxstats code-deduplication: mburnett | 05 September 2013, 15:13:38 UTC |
| 817fded | Mark Burnett | 05 September 2013, 14:19:14 UTC | error_message when no chromosome specified code-deduplication: mburnett | 05 September 2013, 15:13:37 UTC |
| b441af4 | Mark Burnett | 05 September 2013, 14:17:52 UTC | replace temp with query code-deduplication: mburnett | 05 September 2013, 15:13:37 UTC |
| ba065c3 | Mark Burnett | 05 September 2013, 14:16:33 UTC | remove commented code code-deduplication: mburnett | 05 September 2013, 15:13:36 UTC |
| 3262067 | Mark Burnett | 05 September 2013, 14:14:22 UTC | whitespace | 05 September 2013, 15:13:36 UTC |
| 341c32b | Jim Weible | 05 September 2013, 14:37:36 UTC | Create a base class for the somatic VcfMakers code-deduplication: jweible | 05 September 2013, 14:47:03 UTC |
| 3a7370a | Jim Weible | 05 September 2013, 13:25:17 UTC | Refactor out the order_chroms method. code-deduplication: jweible | 05 September 2013, 14:47:03 UTC |
| 0ae174f | Jim Weible | 04 September 2013, 20:13:51 UTC | refactor away genGT method code-deduplication: jweible | 05 September 2013, 14:47:02 UTC |
| 88c0e01 | Jim Weible | 04 September 2013, 20:00:00 UTC | fix type-o | 05 September 2013, 14:47:01 UTC |
| 11790bf | Jim Weible | 04 September 2013, 18:26:21 UTC | Switch to using Genome::Info::IUB in the simplest possible way code-deduplication: jweible | 05 September 2013, 14:47:01 UTC |
| fd0e9ae | Jim Weible | 04 September 2013, 16:08:41 UTC | formatting | 05 September 2013, 14:47:00 UTC |
| 1ec41dd | Thomas Mooney | 05 September 2013, 14:12:18 UTC | Ordering by build_id doesn't work with UUIDs. Use date_scheduled. | 05 September 2013, 14:12:18 UTC |
| 92606ed | Jim Weible | 05 September 2013, 13:59:18 UTC | pass arguments like a sane person | 05 September 2013, 13:59:18 UTC |
| 1fa60b2 | Mark Burnett | 04 September 2013, 22:33:16 UTC | move region_path to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:55 UTC |
| 23b42f9 | Mark Burnett | 04 September 2013, 22:29:59 UTC | move _filter_variants to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:55 UTC |
| a7cba97 | Mark Burnett | 04 September 2013, 22:29:07 UTC | extract filter_status_header code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:54 UTC |
| aa91f24 | Mark Burnett | 04 September 2013, 22:26:33 UTC | extract header_already_added code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:54 UTC |
| 5daef3e | Mark Burnett | 04 September 2013, 22:23:27 UTC | extract should_skip filter from FPVcf code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:53 UTC |
| e6eaa75 | Mark Burnett | 04 September 2013, 22:18:12 UTC | extract should_skip_filter code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:53 UTC |
| 9f8dcfe | Mark Burnett | 04 September 2013, 22:10:23 UTC | extract input_file_path code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:52 UTC |
| 3f8d8df | Mark Burnett | 04 September 2013, 22:06:22 UTC | move output_fh calculation code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:51 UTC |
| 3bab2d8 | Mark Burnett | 04 September 2013, 22:05:06 UTC | extract output_file_path code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:51 UTC |
| 04e5196 | Mark Burnett | 04 September 2013, 21:59:09 UTC | add dummy _convert_to_standard_formats code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:50 UTC |
| 4d66479 | Mark Burnett | 04 September 2013, 21:56:49 UTC | use get_samples_from_header in G:Utility::Vcf code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:50 UTC |
| fda5c61 | Mark Burnett | 04 September 2013, 19:49:53 UTC | move fail_sample to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:49 UTC |
| d098977 | Mark Burnett | 04 September 2013, 19:49:05 UTC | make fail_sample same between classes code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:48 UTC |
| 5ed2c51 | Mark Burnett | 04 September 2013, 19:43:47 UTC | bugfix: don't use "FT" tag for Denovo Vcf Filter | 04 September 2013, 22:39:48 UTC |
| d80f7fa | Mark Burnett | 04 September 2013, 19:38:22 UTC | move generate_and_run_readcounts_in_parallel to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:47 UTC |
| 1f885be | Mark Burnett | 04 September 2013, 19:36:16 UTC | move get_all_sample_names_and_bam_paths and add_per_bam_params_to_input to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:47 UTC |
| a42ac96 | Mark Burnett | 04 September 2013, 19:07:11 UTC | re-order methods to make diff more clear code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:46 UTC |
| 8e46c3d | Mark Burnett | 04 September 2013, 19:00:18 UTC | add questions for gabe code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:46 UTC |
| d0a91af | Mark Burnett | 04 September 2013, 18:58:51 UTC | make fail_sample more similar code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:45 UTC |
| c9e522b | Mark Burnett | 04 September 2013, 18:57:19 UTC | move pass_sample to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:44 UTC |
| a39047a | Mark Burnett | 04 September 2013, 18:56:36 UTC | replace magic "FT"/"DNFT" with method code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:44 UTC |
| 27c4d92 | Mark Burnett | 04 September 2013, 18:55:05 UTC | move filter_one_sample to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:43 UTC |
| 6855fa7 | Mark Burnett | 04 September 2013, 18:45:35 UTC | extract update_variant_for_sample code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:43 UTC |
| 828234d | Mark Burnett | 04 September 2013, 17:22:18 UTC | extract get_readcounts_from_vcf_line to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:42 UTC |
| 4bf1307 | Mark Burnett | 04 September 2013, 17:17:43 UTC | extract get_readcounts_from_vcf_line method code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:41 UTC |
| 042f8d9 | Mark Burnett | 04 September 2013, 17:03:27 UTC | extract filter_sample_format_tag method code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:41 UTC |
| c003cab | Mark Burnett | 04 September 2013, 16:30:58 UTC | make filter_one_line more similar code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:40 UTC |
| 4121ac9 | Mark Burnett | 04 September 2013, 16:27:11 UTC | move required_info_fields to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:39 UTC |
| ebb3d48 | Mark Burnett | 04 September 2013, 16:26:26 UTC | move parse_vcf_header to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:39 UTC |
| c535e22 | Mark Burnett | 04 September 2013, 16:25:30 UTC | extract open_input_file method code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:38 UTC |
| 9fa18e8 | Mark Burnett | 04 September 2013, 16:20:19 UTC | move print_region_list to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:37 UTC |
| b542cd3 | Mark Burnett | 04 September 2013, 16:19:36 UTC | extract should_print_region_line method code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:37 UTC |
| db41c1f | Mark Burnett | 04 September 2013, 16:01:33 UTC | move print_stats to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:36 UTC |
| 8238be8 | Mark Burnett | 04 September 2013, 16:00:46 UTC | move generate_filter_names to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:36 UTC |
| 4986ca6 | Mark Burnett | 04 September 2013, 15:58:56 UTC | move prioritize_allele to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:35 UTC |
| 67627f4 | Mark Burnett | 04 September 2013, 15:58:11 UTC | move convert_numeric_gt_to_alleles to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:35 UTC |
| 4d713db | Mark Burnett | 04 September 2013, 15:56:33 UTC | move get_variant_for_sample to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:34 UTC |
| 2b2b826 | Mark Burnett | 04 September 2013, 15:54:37 UTC | move set_format_field to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:34 UTC |
| 9ad66c6 | Mark Burnett | 04 September 2013, 15:53:36 UTC | move add_filter_to_vcf_header to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:33 UTC |
| db1f7ad | Mark Burnett | 04 September 2013, 15:51:16 UTC | move read_counts_by_allele to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:32 UTC |
| 53ecd9a | Mark Burnett | 04 September 2013, 15:42:26 UTC | move fails_homopolymer_check to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:32 UTC |
| 0bf23b5 | Mark Burnett | 04 September 2013, 15:41:49 UTC | move make_buffered_rc_searcher to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:31 UTC |
| 840bc05 | Mark Burnett | 04 September 2013, 15:40:54 UTC | move _get_readcount_line to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:31 UTC |
| f844d09 | Mark Burnett | 04 September 2013, 15:39:44 UTC | make base class abstract code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:30 UTC |
| 48e8825 | Mark Burnett | 04 September 2013, 15:38:24 UTC | move help to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:29 UTC |
| a306f04 | Mark Burnett | 04 September 2013, 15:36:28 UTC | remove trailing whitespace code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:29 UTC |
| 6caa3c1 | Mark Burnett | 04 September 2013, 15:35:11 UTC | move object properties to base code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:28 UTC |
| 3e3f913 | Mark Burnett | 04 September 2013, 15:31:51 UTC | create empty base class for FalsePositiveVcf* code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:28 UTC |
| 8aaf39e | Mark Burnett | 04 September 2013, 15:27:45 UTC | remove breakpoints code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:27 UTC |
| 12e9335 | Mark Burnett | 04 September 2013, 15:25:35 UTC | increase similarity of FalsePositiveVcf{,Denovo}.pm code-deduplication: gsanders, mburnett | 04 September 2013, 22:39:27 UTC |
