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Implement ReadsHtsgetData source, refactor HtsgetReader #6662

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Implement ReadsHtsgetData source, refactor HtsgetReader #6662

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a476ce7
Implement ReadsHtsgetData source, refactor HtsgetReader
andersleung Jun 16, 2020
ff50eec
Update HtsgetReader command line tests
andersleung Jun 16, 2020
aa4d48a
Commit missing files
andersleung Jun 16, 2020
ba2dd80
Add javadoc, further refactoring to allow easier testing, lazily stre…
andersleung Jun 17, 2020
0cb9530
Use MergingSamRecordIterator internally to ensure proper ordering of …
andersleung Jun 24, 2020
dce337f
Close out all iterators, request headers asynchronously, minor refact…
andersleung Jun 30, 2020
edda05c
Perform map insertion outside of future to avoid concurrent modification
andersleung Jun 30, 2020
3415528
Address PR comments
andersleung Jul 6, 2020
74f7d70
Fix test
andersleung Jul 6, 2020
890da67
WIP Start adding ReadsHtsgetDataSource tests
andersleung Jul 10, 2020
c0cc6ee
Merge branch 'master' into readsHtsgetDataSource
andersleung Jul 10, 2020
8afa04b
WIP fix broken tests
andersleung Jul 13, 2020
946bb4b
WIP Add tests for filtering duplicates, try 127.0.0.1 instead of loca…
andersleung Jul 13, 2020
100b0a4
WIP Try spawning sibling docker container for refserver
andersleung Jul 13, 2020
c6a36cf
WIP try 0.0.0.0:3000 instead of 127.0.0.1
andersleung Jul 13, 2020
1022cbe
WIP Specify 127.0.0.1 in port mapping when running docker
andersleung Jul 13, 2020
062d9ca
WIP configure refserver to listen on 0.0.0.0
andersleung Jul 13, 2020
f166712
WIP configure all IP addresses to 0.0.0.0:3000
andersleung Jul 14, 2020
37eb57d
WIP run test container with net=host
andersleung Jul 14, 2020
1e77370
Add comment to .travis.yml
andersleung Jul 14, 2020
f71ea84
Add end to end tests in PrintReads using htsget source
andersleung Jul 24, 2020
7967843
Merge branch 'master' into readsHtsgetDataSource
andersleung Jul 24, 2020
c437c29
WIP use htsjdk HtsgetBAMFileReader, refactor ReadsPathDataSource to u…
andersleung Aug 18, 2020
27e7dc7
Merge branch 'master' into readsHtsgetDataSource
andersleung Aug 18, 2020
a32a9e3
Add readme to htsgetScripts, move htsget_config.json
andersleung Aug 19, 2020
ea540d1
Remove ReadsHtsgetDataSource and GATK versions of htsget classes
andersleung Aug 19, 2020
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Add comment to .travis.yml
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@andersleung
andersleung committed Jul 14, 2020
commit 1e773704956e11e09fd493e5f92b74e38c1d478e
1 change: 1 addition & 0 deletions .travis.yml
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Expand Up @@ -165,6 +165,7 @@ script:
sudo mkdir -p build/reports/;
sudo chmod -R a+w build/reports/;
cp scripts/docker/dockertest.gradle .;
# Use host network so other docker containers can be reached
sudo docker run --net=host -v $(pwd):/gatkCloneMountPoint:cached -v $(pwd)/testJars:/jars:cached --rm -e "scala.version=${SCALA_VERSION}" -e "TEST_VERBOSITY=minimal" -e "TEST_TYPE=${TEST_TYPE}" -t broadinstitute/gatk:${DOCKER_TAG} bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh;
TEST_EXIT_VALUE=$?;
sudo mkdir build/reports/tests/test && sudo cp -rp build/reports/tests/testOnPackagedReleaseJar/* build/reports/tests/test && sudo rm -r build/reports/tests/testOnPackagedReleaseJar;
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