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add microbial mode #6694

Merged
merged 18 commits into from
Aug 2, 2021
Merged

add microbial mode #6694

merged 18 commits into from
Aug 2, 2021

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ahaessly
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@ahaessly ahaessly commented Jul 2, 2020

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gatk-bot commented Jul 2, 2020 •
edited

Travis reported job failures from build 30874
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 30874.14 logs
unit openjdk8 30874.3 logs
variantcalling openjdk8 30874.4 logs
variantcalling openjdk8 30874.4 logs

@jamesemery jamesemery force-pushed the je_allowMoreMismatchesInDanglingHeadRecovery branch from 1ee14e0 to e8c4972 Compare September 30, 2020 20:02
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gatk-bot commented Oct 1, 2020 •
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Travis reported job failures from build 31583
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Test Type JDK Job ID Logs
unit openjdk11 31583.13 logs
variantcalling openjdk8 31583.4 logs
unit openjdk8 31583.3 logs
unit openjdk8 31583.3 logs

@jamesemery jamesemery force-pushed the je_allowMoreMismatchesInDanglingHeadRecovery branch from e8c4972 to fa3240a Compare November 16, 2020 20:33
@ahaessly ahaessly force-pushed the ah_je_microbial branch 2 times, most recently from 4c6f006 to ff60e32 Compare November 17, 2020 15:36
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gatk-bot commented Nov 17, 2020 •
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Travis reported job failures from build 32145
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cloud openjdk8 32145.1 logs
variantcalling openjdk8 32145.4 logs
unit openjdk8 32145.3 logs

Base automatically changed from je_allowMoreMismatchesInDanglingHeadRecovery to master January 26, 2021 18:47
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Travis reported job failures from build 32643
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variantcalling openjdk8 32643.4 logs

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Travis reported job failures from build 32648
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variantcalling openjdk8 32648.4 logs

@ahaessly ahaessly marked this pull request as ready for review January 28, 2021 17:31
@ahaessly ahaessly requested a review from droazen January 28, 2021 17:32
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gatk-bot commented Jan 28, 2021 •
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Travis reported job failures from build 32664
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Test Type JDK Job ID Logs
variantcalling openjdk8 32664.4 logs
variantcalling openjdk8 32664.4 logs

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droazen commented Feb 4, 2021

@ahaessly I've asked @jamesemery to review, as this touches some of his code. In the mean time, though, could you please add at least one good integration test for the new ShiftFasta tool?

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A bunch of minor comments. It would generally be nice for there to be more comments and method documentation in the tool you added. More importantly I think we really need to have at least a simple integration test for that tool that at the very least asserts it does something reasonable on some fasta (it doesn't have to be a real file you can just use some dummy fasta files).

...itute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java Show resolved Hide resolved
...itute/hellbender/tools/walkers/haplotypecaller/readthreading/AbstractReadThreadingGraph.java Outdated Show resolved Hide resolved
...rg/broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java Outdated
@@ -43,6 +43,13 @@
@Argument(fullName = M2ArgumentCollection.MITOCHONDRIA_MODE_LONG_NAME, optional = true, doc = "Set filters to mitochondrial defaults")
public boolean mitochondria = false;

/**
* Mitochondria mode excludes the filters {@link ClusteredEventsFilter}, {@link MultiallelicFilter},
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Can you update this list to be comprehensive to all the changes?

Also were you not going to make this argument affect the graph code at all? I thought bacterial mode would want to use the new dangling end pruning code and that doesn't seem to be linked to microbial mode at all.

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This also doesn't refrence the median mapping wquality change.

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right now that flag is specified in the wdl for microbial mutect. We may decide to add it to the code when using this mode in a later PR

...rg/broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java Outdated Show resolved Hide resolved
...rg/broadinstitute/hellbender/tools/walkers/mutect/filtering/M2FiltersArgumentCollection.java Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java Show resolved Hide resolved
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gatk-bot commented Mar 15, 2021 •
edited

Travis reported job failures from build 33205
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 33205.13 logs
unit openjdk8 33205.3 logs
variantcalling openjdk8 33205.4 logs

jamesemery and others added 8 commits March 19, 2021 13:53
@jamesemery @ahaessly
rebased version of this code
0558f71
@jamesemery @ahaessly
fixed an issue where the logic for suffix ends was incorrect for dang…
c7d014f 
…ling tails
@jamesemery @ahaessly
responding to review comments
dd6907d
@ahaessly
manual rebase
e94783a
@ahaessly
change misspellings of dangling to the correct spelling
e3865a0
@ahaessly
remove change from bad merge
14f82ae
@ahaessly
parent 6d43103
e389981 
author Andrea Haessly <[email protected]> 1582141271 -0500
committer Andrea Haessly <[email protected]> 1611852899 -0500

parent 6d43103
author Andrea Haessly <[email protected]> 1582141271 -0500
committer Andrea Haessly <[email protected]> 1611852778 -0500

initial impl
tested shift and chain
make offset optional
fix format of chain file
make offset optional
fix format of chain file
add interval output
@ahaessly
check for is empty
a4f8290
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gatk-bot commented Mar 19, 2021 •
edited

Travis reported job failures from build 33270
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud openjdk8 33270.1 logs
cloud openjdk11 33270.14 logs

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gatk-bot commented Mar 19, 2021 •
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Travis reported job failures from build 33268
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cloud openjdk11 33268.14 logs
unit openjdk11 33268.13 logs
unit openjdk8 33268.3 logs
variantcalling openjdk8 33268.4 logs

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gatk-bot commented Mar 22, 2021 •
edited

Travis reported job failures from build 33279
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Test Type JDK Job ID Logs
cloud openjdk11 33279.14 logs
cloud openjdk8 33279.1 logs

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Travis reported job failures from build 35083
Failures in the following jobs:

Test Type JDK Job ID Logs
variantcalling openjdk8 35083.4 logs

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jamesemery reviewed Jul 23, 2021
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Just a few very minor comments to address/answer then i think this can be merged

src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java Outdated Show resolved Hide resolved
src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFastaTest.java Outdated Show resolved Hide resolved
src/test/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFastaTest.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/fasta/ShiftFasta.java Show resolved Hide resolved
.../org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/AdaptiveChainPruner.java Show resolved Hide resolved
@ahaessly
this changes the behavior of the adaptive pruner at low/patchy refere…
c0c5474 
…nce coverage sites\nAdd large files to resources
@ahaessly ahaessly requested a review from jamesemery July 27, 2021 17:57
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jamesemery approved these changes Jul 27, 2021
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This looks good to me. Feel free to merge when tests pass!

@ahaessly ahaessly merged commit f548ccd into master Aug 2, 2021
@ahaessly ahaessly deleted the ah_je_microbial branch August 2, 2021 17:03
@lbergelson lbergelson mentioned this pull request Dec 8, 2021
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@jamesemery jamesemery jamesemery approved these changes

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