Added a useful debugging output mode that prints a summary of every assembly region #6441

jamesemery · 2020-02-04T19:35:36Z

This is intended for debugging purposes.

gatk-bot · 2020-02-04T20:16:52Z

Travis reported job failures from build 28970
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	openjdk11	28970.13	logs
unit	openjdk8	28970.3	logs

gatk-bot · 2020-02-04T20:22:07Z

Travis reported job failures from build 28972
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	openjdk11	28972.13	logs
unit	openjdk8	28972.3	logs

droazen · 2020-02-05T17:02:38Z

@davidbenjamin Care to have a look at this one?

davidbenjamin

Back to @jamesemery

...r/tools/walkers/haplotypecaller/HaplotypeCallerReadThreadingAssemblerArgumentCollection.java

...itute/hellbender/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java

...institute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java

...broadinstitute/hellbender/tools/walkers/variantutils/SummarizeActiveRegionOutAgainstVCF.java

davidbenjamin · 2020-02-05T19:35:29Z

...broadinstitute/hellbender/tools/walkers/variantutils/SummarizeActiveRegionOutAgainstVCF.java

+        List<VariantContext> overlappingVariants = featureContext.getValues(overlappingVariantInput);
+
+        outputTableWriter.getNewLineBuilder()
+                .setColumn("active_region", feature.get("active_region"))


Is there any way to write this more explicitly as appending the count of overlapping variants to the input feature?

.../broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

...hellbender/tools/walkers/variantutils/SummarizeActiveRegionOutAgainstVCFIntegrationTest.java

davidbenjamin · 2020-02-05T19:37:29Z

...hellbender/tools/walkers/variantutils/SummarizeActiveRegionOutAgainstVCFIntegrationTest.java

+        final File inputAssemblyRegion = new File(TEST_FILES_DIR, "testAssemblyRegionOutput.table");
+        final File inputVCF = new File(TEST_FILES_DIR, "expected.testVCFMode.gatk4.vcf");
+
+        final String[] args = {


An ArgumentsBuilder would be cleaner

davidbenjamin · 2020-02-05T19:41:41Z

...institute/hellbender/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java

+        if ( debugActiveRegionOutputStream != null ) {
+            debugActiveRegionOutputStream.getNewLineBuilder()
+                .setRow(new String[]{
+                        assemblyRegion.getSpan().toString(),


What would you think about a boolean option to use getExtendedSpan, which would give you the intervals (possibly overlapping) over which the GATK assembled? I could imagine that being useful, too.

I see two options here, both are potentially useful. I ask your opinion between the two. FIrst, I could add a second argument flag that dictates what level of padding gets included (which could possibly be expanded in the future). Second (and probably my preference) would be to add these as another column in the output of the file (say: unpadded_region) so the information would always be accessable.

Let's go with the second option.

it is now an extra column in every case. This will allow people to use either line they please if they use their bash magic to extract it, which is ultimately the goal here.

jamesemery · 2020-02-07T16:40:44Z

@davidbenjamin back to you

davidbenjamin · 2020-02-07T17:06:38Z

👍

gatk-bot · 2020-02-07T17:20:01Z

Travis reported job failures from build 29031
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	openjdk11	29031.13	logs
unit	openjdk8	29031.3	logs

…data for the future Created a dummy tool to add a new annotation to my table file so I can produce a pretty plot added a hack to make the reading work

…ncorrectly

gatk-bot · 2020-02-28T20:54:44Z

Travis reported job failures from build 29307
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	openjdk11	29307.14	logs
variantcalling	openjdk8	29307.4	logs
unit	openjdk8	29307.3	logs

gatk-bot · 2020-02-28T21:03:59Z

Travis reported job failures from build 29311
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	openjdk11	29311.14	logs
unit	openjdk8	29311.3	logs

jamesemery requested a review from lbergelson February 4, 2020 19:35

droazen requested a review from davidbenjamin February 5, 2020 17:02

droazen assigned davidbenjamin Feb 5, 2020

davidbenjamin requested changes Feb 5, 2020

View reviewed changes

davidbenjamin added assembly enhancement labels Feb 6, 2020

jamesemery force-pushed the je_addAssemblyRegionOutFileToGraph branch from 31cdd0d to 35fe0ec Compare February 7, 2020 16:40

davidbenjamin approved these changes Feb 7, 2020

View reviewed changes

jamesemery added 6 commits February 28, 2020 15:00

added a command for printing out active regions in order to generate …

0076f4a

…data for the future Created a dummy tool to add a new annotation to my table file so I can produce a pretty plot added a hack to make the reading work

adding tests that these features at least function in the abstract

6e5824b

fixed a silly issue with the dummy class

aed5c1b

responded to comments

fadb444

one more extraction

3307352

fixed the rebaseconfusion

1221ebb

jamesemery force-pushed the je_addAssemblyRegionOutFileToGraph branch from 35fe0ec to 1221ebb Compare February 28, 2020 20:16

clearing up an issue with the assembly result set kmers being added i…

767ee62

…ncorrectly

conforming the table codec to a reasonable format

2708910

davidbenjamin assigned jamesemery and unassigned davidbenjamin Jun 9, 2020

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Added a useful debugging output mode that prints a summary of every assembly region #6441

Added a useful debugging output mode that prints a summary of every assembly region #6441

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Added a useful debugging output mode that prints a summary of every assembly region #6441

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Added a useful debugging output mode that prints a summary of every assembly region #6441

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