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Commits on Sep 18, 2018

• Update SmithWaterman and Pairhmm on gatk4 java files

  

  Yinhe Cheng [email protected]

  committed
  1ba826c

Commits on Sep 17, 2018

• Merge pull request #1 from broadinstitute/master

  Show description for 54e1bdc
  yhcheng

  authored
  54e1bdc

• M2 emits DP format field (broadinstitute#5185)

  davidbenjamin

  authored
  0619f17

• fix 5183 (broadinstitute#5184)

  davidbenjamin

  authored
  4aac7a4

• Fixed ref conf calculation upstream of indel (broadinstitute#5172)

  Show description for 21f16d5
  ldgauthier

  authored
  21f16d5

Commits on Sep 14, 2018

• Move/rename some stray Spark datasource classes, and delete BaseRecalibratorSparkSharded (broadinstitute#5192)

  Show description for c935dc7
  droazen

  authored
  c935dc7

• Port LeftAlignAndTrimVariants from GATK3 (broadinstitute#5144)

  

  kachulis

  authored and

  jamesemery

  committed
  60f383d

• change maven badge to use shields IO (broadinstitute#5191)

  Show description for dd93c02
  lbergelson

  authored
  dd93c02

Commits on Sep 13, 2018

• Added documentation warnings about empty clipped reads from readClipper where they can occur (broadinstitute#4212)

  Show description for 0e95bfb
  

  jamesemery

  authored and

  droazen

  committed
  0e95bfb

• Skip push builds if there is a pull request (broadinstitute#5156)

  Show description for 678ab2d
  lbergelson

  authored
  678ab2d

• Updated COSMIC to annotate protein change strings with their counts. (broadinstitute#5181)

  Show description for 9146f70
  jonn-smith

  authored
  9146f70

• Added optional mappability and segmental-duplication annotation to AnnotateIntervals. (broadinstitute#5162)

  Show description for 63f7b63
  samuelklee

  authored
  63f7b63

• Added better error messages around missing ReadGroups in MarkDuplicatesSpark (broadinstitute#5177)

  jamesemery

  authored
  5a09b88

Commits on Sep 11, 2018

• Upgrade Picard from 2.18.7 -> 2.18.13. (broadinstitute#5173)

  cmnbroad

  authored
  d6e762e

Commits on Sep 10, 2018

• Created a FuncotatorDataSourceRetriever to download data sources. (broadinstitute#5150)

  Show description for 575f11d
  jonn-smith

  authored
  575f11d

• Fix some AlignmentUtils issues (broadinstitute#3494)

  Show description for 41d72b7
  

  DonFreed

  authored and

  droazen

  committed
  41d72b7

• Removed experimental tool MarkDuplicatesGATK in favor of MarkDuplicatesSpark (broadinstitute#5166)

  jamesemery

  authored
  2386612

Commits on Sep 7, 2018

• upgrading to htsjdk 2.16.1 (broadinstitute#5168)

  lbergelson

  authored
  c5744b6

• Switched MarkDuplicatesSpark tile parsing code to use shorts in order to match picard (broadinstitute#5165)

  jamesemery

  authored
  83832ea

Commits on Sep 6, 2018

• Fix Edge Cases in Reference Bases (broadinstitute#5151)

  Show description for 813e593
  

  takutosato

  authored and

  droazen

  committed
  813e593

• cnn variant wdls and jsons (broadinstitute#4774)

  Show description for 6d0ca0f
  lucidtronix

  authored
  6d0ca0f

• documentation clarification to SVInterval, also requires constructor argument validator (broadinstitute#5157)

  SHuang-Broad

  authored
  2bfe742

Commits on Sep 5, 2018

• Make HaplotypeCaller genotype and output spanning deletions (broadinstitute#4963)

  Show description for 33af6de
  cwhelan

  authored
  33af6de

• Share the test settings between the main build and the docker tests (broadinstitute#5155)

  

  lbergelson

  authored and

  jamesemery

  committed
  2b739e9

• Clone read base qualities rather than reference them in the read clipper to prevent unsafe array operations (broadinstitute#4926)

  

  DonFreed

  authored and

  jamesemery

  committed
  916d0ab

Commits on Sep 4, 2018

• Enable Requester Pays support (broadinstitute#5140)

  Show description for e6f1c6b
  

  jean-philippe-martin

  authored and

  droazen

  committed
  e6f1c6b

• Adds a class to represent expected insert-size distribution (normal a… (broadinstitute#4827)

  Show description for 01d5ea2
  

  Valentin Ruano Rubio

  authored
  01d5ea2

Commits on Aug 31, 2018

• Updated datasource version parsing (broadinstitute#5149)

  Show description for 006b1b9
  jonn-smith

  authored
  006b1b9

• Restore base quality filter code that got reverted in broadinstitute#4895. Reduce duplicated code in tests surrounding Mutect2. (broadinstitute#5123)

  takutosato

  authored
  9fb2a65

Commits on Aug 30, 2018

• Fix to Enable SelectVariants to drop sites with * allele as only ALT (broadinstitute#5129)

  Show description for 36d20c7
  kvinter1

  authored
  36d20c7

• Simplify HaplotypeBAMWriter code. broadinstitute#944 (broadinstitute#5122)

  

  kvinter1

  authored and

  cmnbroad

  committed
  da950e2

Commits on Aug 28, 2018

• Added Called Legacy Segment code (broadinstitute#5115)

  Show description for 63d4287
  LeeTL1220

  authored
  63d4287

• Updated VCF gencode annotation positions/alleles. (broadinstitute#5131)

  Show description for fea2c8d
  jonn-smith

  authored
  fea2c8d

• Document use of --temp-dir with GenomicsDB. (broadinstitute#5047)

  

  Jake VanCampen

  authored and

  cmnbroad

  committed
  23f6f08

Commits on Aug 27, 2018

• VQSR serialized model sets annotation order (broadinstitute#3655)

  Show description for d2e2580
  lucidtronix

  authored
  d2e2580

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