ExtractCohort supports -XL exclusion and follows intervals, other optimizations #7181

mmorgantaylor · 2021-04-02T19:11:28Z

added custom classes ExtractCohortRecord and ExtractCohortFilterRecord that implement Locatable
refactored attribute building from these records
now that the records are Locatables, can use OverlapDetector to filter locations down to only desired intervals (including excluded sites)
removed queryMode QUERY and associated querying from options

...org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortFilterRecordUnitTest.java

mmorgantaylor · 2021-04-05T15:52:58Z

...org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortFilterRecordUnitTest.java

+
+    @Test
+    public void testGetContig() {
+        String expectedContig = "chr1";


is it preferred to define these single-use objects explicitly or just stick "chr1" into the assertion statement directly?

either way is fine. I tend to put them right in the assertion so it's easier to read if I'm not also using it to construct the test data. In that case I pull it out so I don't have "chr1" repeated throughout the method

yeah reading the rest of these tests I would just inline it into the assert for readability

...org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortFilterRecordUnitTest.java

kcibul

Great refactoring

src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohort.java

kcibul · 2021-04-02T20:02:56Z

src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java

-                final Allele alt = Allele.create(queryRow.get("alt").toString(), false);
+                final ExtractCohortFilterRecord filterRow = new ExtractCohortFilterRecord( queryRow );
+
+                final long location = filterRow.getLocation();


src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java

kcibul · 2021-04-02T20:04:11Z

src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java

-            sampleRecords.add(new QueryRecord(row));
-
+                // TODO remove queryMode entirely from ExtractTool
+                throw new NotImplementedException("QUERY mode not supported. Please use `--query-mode LOCAL_SORT`.");


src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortEngine.java

...org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortFilterRecordUnitTest.java

kcibul · 2021-04-05T16:54:49Z

...org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortFilterRecordUnitTest.java

+
+    @Test
+    public void testGetContig() {
+        String expectedContig = "chr1";


either way is fine. I tend to put them right in the assertion so it's easier to read if I'm not also using it to construct the test data. In that case I pull it out so I don't have "chr1" repeated throughout the method

kcibul · 2021-04-05T16:55:43Z

...org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortFilterRecordUnitTest.java

+
+    @Test
+    public void testGetContig() {
+        String expectedContig = "chr1";


yeah reading the rest of these tests I would just inline it into the assert for readability

.../java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortRecordUnitTest.java

gatk-bot · 2021-04-05T21:22:52Z

Travis reported job failures from build 33556
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	openjdk8	33556.1	logs
cloud	openjdk11	33556.14	logs

mmorgantaylor requested review from kcibul and ahaessly April 2, 2021 19:11

mmorgantaylor commented Apr 5, 2021

View reviewed changes

...org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractCohortFilterRecordUnitTest.java Outdated Show resolved Hide resolved

mmorgantaylor commented Apr 5, 2021

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kcibul approved these changes Apr 5, 2021

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mmorgantaylor force-pushed the mmt_extract_cohort_records branch from 5b065b1 to 22fe7fc Compare April 5, 2021 20:55

mmorgantaylor added 17 commits April 6, 2021 13:19

send traversalIntervals to ExtractCohortEngine

a6247bf

refactor for ExtractCohortRecord, add OverlapDetector

6af2440

handle null values

3a68376

minor cleanup

455f46a

test add vqslod

1c73df2

add ExtractCohortFilterRecord

3f83566

remove querymode QUERY from ExtractCohort

0b64a08

cleanup

5108b31

more cleanup

d138009

add unit tests, fix minor bug in ExtractCohortFilterRecord, cleanup

301a089

test from avro file for ExtractCohortRecord

146d010

read input from avro for ExtractCohortFilterRecord, clean up

d3a90f7

addressing code review comments

2f41442

remove println line

9f414b9

inlinification

0f8354b

more intuitive test names, whitespace cleanup

f11fa6e

fix ExtractCohortRemoveAnnotationsUnitTest

fc31d94

mmorgantaylor force-pushed the mmt_extract_cohort_records branch from 22fe7fc to fc31d94 Compare April 6, 2021 17:21

mmorgantaylor merged commit 2cbfc3a into ah_var_store Apr 6, 2021

mmorgantaylor deleted the mmt_extract_cohort_records branch April 6, 2021 19:04

This was referenced Mar 17, 2023

lb merge gvs branch #8248

Closed

testing something, please ignore #8251

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ExtractCohort supports -XL exclusion and follows intervals, other optimizations #7181

ExtractCohort supports -XL exclusion and follows intervals, other optimizations #7181

mmorgantaylor commented Apr 2, 2021 •

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ExtractCohort supports -XL exclusion and follows intervals, other optimizations #7181

ExtractCohort supports -XL exclusion and follows intervals, other optimizations #7181

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