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Test out the preview version of the next GKL (DO NOT MERGE) #8712

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Test out the preview version of the next GKL (DO NOT MERGE) #8712

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df9d19a
Add in the preview GKL build as a dependency
droazen Mar 4, 2024
5e6bd62
Added the java code to wrap the IntelPDPairHMM implementation for DRA…
jamesemery Mar 6, 2024
fe4a60d
Switch to gkl-0.8.11-3-g26de538-SNAPSHOT.jar
droazen Apr 24, 2024
1952912
Switch to gkl-2024_05_31, incorporate Intel patch to VectorLoglessPai…
droazen May 31, 2024
b1d7994
Temporarily revert Intel patch to VectorLoglessPairPDHMM.java, for te…
droazen Jul 19, 2024
4bd2d71
Restore one-line Intel patch to VectorLoglessPairPDHMM
droazen Jul 22, 2024
5997b30
added some debugging for figuring out what is going on with the gkl m…
jamesemery Jul 22, 2024
4ee399b
error
jamesemery Jul 22, 2024
cacf20d
adding quick remote test
jamesemery Jul 23, 2024
62bc0ce
;
jamesemery Jul 23, 2024
0217486
of course i can't run this anywhere
jamesemery Jul 23, 2024
e5dc0a4
piggybacking off of one that may have worked past?
jamesemery Jul 23, 2024
54dff49
more permissions
jamesemery Jul 23, 2024
fecf938
why didn't that last one work?
jamesemery Jul 23, 2024
bc68361
group
jamesemery Jul 23, 2024
c366995
restart? hopefully transient
jamesemery Jul 24, 2024
f2fb477
Refactored the interface to the new GKL JNI to batch submissions to a…
jamesemery Jul 25, 2024
a2d32bd
two tweeks and one bug
jamesemery Jul 25, 2024
545907f
yet more guardrails
jamesemery Jul 25, 2024
a67d8b3
assert failure
jamesemery Jul 26, 2024
cbd4bde
testing limits for batches
jamesemery Jul 29, 2024
a1a431b
Switch to latest GKL build (2024-08-08)
droazen Aug 8, 2024
7874846
update to test new jar
lbergelson Sep 23, 2024
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why didn't that last one work?
@jamesemery
jamesemery committed Jul 23, 2024
commit fecf93813a3d61a6e953e45aab9bd95c58e8c5aa
2 changes: 1 addition & 1 deletion ...oadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View file
Original file line number Diff line number Diff line change
@@ -2164,7 +2164,7 @@ public void testPileupCallingDRAGEN378OptimizedModeConsistentWithPastResults(fin
final File output = createTempFile("testVCFModeIsConsistentWithPastResults", ".vcf");
final File expected = new File(TEST_FILES_DIR, "expected.pileupCallerDRAGEN.378.gatk4.vcf");

final String outputPath = "gs://hellbender-test-logs/staging/emeryj/foo.vcf"; //UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();
final String outputPath = "gs://hellbender-test-logs/staging/emeryj/test-foo.vcf"; //UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();

final String[] args = {
"-I", inputFileName,