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14489 Commits (c855714e10be425f94416bbb561e1f39c84d1085)

Author SHA1 Message Date
ldgauthier c855714e10 Merge pull request #1586 from broadinstitute/ldg_turnOffOneMoreTest 
One more stupid fargo bam test to turn off
 2017-05-11 12:17:11 -04:00
Laura Gauthier 417d390077 One more stupid fargo bam test to turn off 2017-05-11 09:54:38 -04:00
ldgauthier ae174d3359 Merge pull request #1541 from broadinstitute/ldg_revertToMedianRankSum 
Changed calculation of allele-specific rank sum so it's now the median of the per-sam…
 2017-05-10 14:43:08 -04:00
Laura Gauthier 35d0b72c79 Changed calculation of rank sum so it's now the median of the per-sample rank sums (because the rank sum across all sample data did worse for biallelics). Now only called alt for 0/1s has rank sum, similar to old paradigm. Combined gVCF rank sums stored in Histogram, then median is taken once during genotyping. Histogram uses Integer keys to eliminate numerical precision mess 2017-05-10 09:04:42 -04:00
ldgauthier d512f3f808 Merge pull request #1582 from broadinstitute/SC-input-prior-HC-doc-fix 
Change AC>1 to AC>0
 2017-05-09 14:15:42 -04:00
Sheila Chandran 8703642142 Change AC>1 to AC>0 2017-05-09 13:31:58 -04:00
Samuel Friedman 00b7135afe Merge pull request #1575 from broadinstitute/snf_ReadGMMReport 
Read model report and reconstruct GMM from it in VQSR
 2017-05-08 14:40:27 -04:00
Samuel Friedman ed440f1684 respond to review comments 2017-05-05 16:29:01 -04:00
Samuel Friedman 68bdb93c8c add annotation mismatch warning and refactor tests 2017-05-04 16:48:24 -04:00
Samuel Friedman f5d133df87 scientific notation in model report and basic test 2017-05-03 18:37:52 -04:00
ldgauthier e9efd53281 Merge pull request #1581 from broadinstitute/ldg_actuallyFixTests 
Turn off one more test that needs the fargo bam
 2017-05-03 09:59:20 -04:00
Laura Gauthier c91cacb642 Turn off one more unit test with fargo bam 2017-05-03 09:53:08 -04:00
droazen 67cf29558f Merge pull request #1578 from broadinstitute/ldg_turnOffPicardAggregationTests 
Turn off PicardAggregation tests because they're a pain with all the …
 2017-05-02 16:20:35 -04:00
Samuel Friedman 4df71a3ca1 expect floats in the report 2017-05-02 12:05:10 -04:00
Ron Levine 505383e504 Remove obsolete unmapped reads test for FindCoveredIntervals (#1580) 
Remove obsolete unmapped reads test for FindCoveredIntervals
 2017-05-02 08:50:12 -04:00
Samuel Friedman 1b4ac51048 move model file parsing to initialize 2017-05-01 15:52:45 -04:00
Laura Gauthier 2284a69e7c Turn off PicardAggregation tests because they're a pain with all the bams moving to slow storage and because the pipeline utils aren't used anyway 2017-04-29 09:20:57 -04:00
Samuel Friedman d06a6c7318 string cast bug 2017-04-28 17:32:36 -04:00
meganshand 31eee1f2a3 Merge pull request #1576 from broadinstitute/ms_FS_bug 
Fixes rounding errors in FS using the same solution as R
 2017-04-28 17:02:09 -04:00
meganshand ea5efa0b2c Fixes rounding errors in FS using the same solution as R 2017-04-27 17:37:33 -04:00
Samuel Friedman f55b932cfc addressed review comments 2017-04-27 17:16:57 -04:00
Samuel Friedman 85cb1c2810 dont spam on NaNs 2017-04-26 17:33:06 -04:00
Samuel Friedman 57c064eaa3 small code cleanup 2017-04-26 16:02:06 -04:00
Samuel Friedman a8f70c891f Create GMM from model reports in VQSR 2017-04-26 16:02:06 -04:00
skwalker 4fe4ace232 minor bug fix in depth of coverage for partitioning by library + test (#1574) 
minor bug fix in depth of coverage for partitioning by library
 2017-04-26 10:42:54 -04:00
droazen 5110b13124 Merge pull request #1572 from broadinstitute/dr_use_gkl_intel_inflater_deflater 
Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default
 2017-04-14 16:22:34 -04:00
David Roazen a950d0778f Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default 2017-04-05 12:45:26 -04:00
Ron Levine 728b3db8e0 Merge pull request #1571 from broadinstitute/rhl_vtbp_doc_1570 
Update PLINK link and change lines to columns
 2017-03-23 14:22:05 -04:00
Ron Levine 278985b8bd Update PLINK link and change lines to columns 2017-03-23 11:46:38 -04:00
Ron Levine 485a090ef6 Merge pull request #1569 from broadinstitute/rhl_vtt_doc_orders_samples_1545 
Document how VTT orders samples in output table
 2017-03-21 18:09:35 -04:00
Ron Levine 00a434a38b Merge pull request #1568 from broadinstitute/rhl_mutect2_doc_germline_1560 
Update MuTect2 documentation about not computing obvious germline variants
 2017-03-21 18:08:39 -04:00
Ron Levine 4188745074 Document how VTT orders samples in output table 2017-03-21 18:04:38 -04:00
Ron Levine c20e682a97 Update MuTect2 documentation about not computing obvious germline variants 2017-03-21 17:54:52 -04:00
Ron Levine c449b133d0 Merge pull request #1565 from broadinstitute/rhl_fix_cv_merge_1547 
Fix CombineVariants merge for different types
 2017-03-14 16:43:33 -04:00
Ron Levine 687dee22ac Fix CombineVariants merge for different types 2017-03-14 16:42:16 -04:00
Ron Levine 31315a31c0 Merge pull request #1563 from broadinstitute/rhl_fci_thresholds_1562 
Fix FindCoveredIntervals so -minBQ, -minMQ and -cov work as expected
 2017-03-07 17:07:45 -05:00
Ron Levine 49083fc704 Fix FindCoveredIntervals so -minBQ, -minMQ and -cov work as expected 2017-03-07 16:58:23 -05:00
Ron Levine b3df32047f Merge pull request #1535 from broadinstitute/rhl_clipping_op_align_offset_1447 
Fixed ClippingOP.getNewAlignmentStartOffset() to handle N cases properly
 2017-03-06 17:53:12 -05:00
Ron Levine 1e88d849e3 Fixed ClippingOP.getNewAlignmentStartOffset() to handle N cases properly and added unit test 2017-03-06 15:40:01 -05:00
Ron Levine faeac6e5a4 Merge pull request #1551 from broadinstitute/rhl_hc_no_dp_ad_1322 
Set AD and DP to zero if no read coverage
 2017-02-28 16:58:21 -05:00
Ron Levine 8316fa92f3 Set AD and DP to zero if no read coverage 2017-02-28 16:56:45 -05:00
Ron Levine c0bf07cb78 Merge pull request #1559 from broadinstitute/rhl_htsjdk_2.9.1_picard_2.9.0 
Move htsjdk to ver 2.9.1 and picard to ver 2.9.0
 2017-02-23 14:32:44 -05:00
Ron Levine 91339c12c9 Move htsjdk to ver 2.9.1 and picard to ver 2.9.0 2017-02-22 19:01:26 -05:00
Ron Levine 5c178c2a84 Merge pull request #1553 from broadinstitute/rhl_latv_split_nocall_1518 
Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref
 2017-02-22 18:54:26 -05:00
Ron Levine 61875e4dfa Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref 2017-02-22 17:57:59 -05:00
Ron Levine b9a43cc35e Merge pull request #1557 from broadinstitute/rhl_ggvcfs_input_prior_1532 
Total ploidy does not have to equal to the number of priors
 2017-02-20 22:21:25 -05:00
Ron Levine 3c347c1385 Total ploidy does not have to equal to the number of priors 2017-02-20 20:28:41 -05:00
Ron Levine c55c77ab27 Merge pull request #1555 from broadinstitute/rhl_htsjdk_2.9.0_picard_2.8.3 
Move htsjdk to ver 2.9.0 and picard to ver 2.8.3
 2017-02-17 13:54:17 -05:00
Ron Levine ab75b08ea7 Remove unused compressed_block_size and close BlockCompressedInputStream 2017-02-17 12:22:53 -05:00
Ron Levine 1d36d9fd69 Move htsjdk to ver 2.9.0 and picard to ver 2.8.3 2017-02-17 07:03:03 -05:00