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Implement ReadsHtsgetData source, refactor HtsgetReader #6662

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Implement ReadsHtsgetData source, refactor HtsgetReader #6662

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Commits on Jun 16, 2020

  1. Implement ReadsHtsgetData source, refactor HtsgetReader

    @andersleung
    andersleung committed Jun 16, 2020
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  2. Update HtsgetReader command line tests

    @andersleung
    andersleung committed Jun 16, 2020
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  3. Commit missing files

    @andersleung
    andersleung committed Jun 16, 2020
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Commits on Jun 17, 2020

  1. Add javadoc, further refactoring to allow easier testing, lazily stre… 

    …am htsget data
    @andersleung
    andersleung committed Jun 17, 2020
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Commits on Jun 24, 2020

  1. Use MergingSamRecordIterator internally to ensure proper ordering of … 

    …reads
    @andersleung
    andersleung committed Jun 24, 2020
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Commits on Jun 30, 2020

  1. Close out all iterators, request headers asynchronously, minor refact… 

    …oring
    @andersleung
    andersleung committed Jun 30, 2020
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  2. Perform map insertion outside of future to avoid concurrent modification

    @andersleung
    andersleung committed Jun 30, 2020
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Commits on Jul 6, 2020

  1. Address PR comments

    @andersleung
    andersleung committed Jul 6, 2020
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  2. Fix test

    @andersleung
    andersleung committed Jul 6, 2020
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Commits on Jul 10, 2020

  1. WIP Start adding ReadsHtsgetDataSource tests

    @andersleung
    andersleung committed Jul 10, 2020
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  2. Merge branch 'master' into readsHtsgetDataSource

    @andersleung
    andersleung committed Jul 10, 2020
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Commits on Jul 13, 2020

  1. WIP fix broken tests

    @andersleung
    andersleung committed Jul 13, 2020
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  2. WIP Add tests for filtering duplicates, try 127.0.0.1 instead of loca… 

    …lhost
    @andersleung
    andersleung committed Jul 13, 2020
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  3. WIP Try spawning sibling docker container for refserver

    @andersleung
    andersleung committed Jul 13, 2020
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  4. WIP try 0.0.0.0:3000 instead of 127.0.0.1

    @andersleung
    andersleung committed Jul 13, 2020
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  5. WIP Specify 127.0.0.1 in port mapping when running docker

    @andersleung
    andersleung committed Jul 13, 2020
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  6. WIP configure refserver to listen on 0.0.0.0

    @andersleung
    andersleung committed Jul 13, 2020
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Commits on Jul 14, 2020

  1. WIP configure all IP addresses to 0.0.0.0:3000

    @andersleung
    andersleung committed Jul 14, 2020
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  2. WIP run test container with net=host

    @andersleung
    andersleung committed Jul 14, 2020
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  3. Add comment to .travis.yml

    @andersleung
    andersleung committed Jul 14, 2020
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Commits on Jul 24, 2020

  1. Add end to end tests in PrintReads using htsget source

    @andersleung
    andersleung committed Jul 24, 2020
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  2. Merge branch 'master' into readsHtsgetDataSource

    @andersleung
    andersleung committed Jul 24, 2020
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Commits on Aug 18, 2020

  1. WIP use htsjdk HtsgetBAMFileReader, refactor ReadsPathDataSource to u… 

    …se GATKPath
    @andersleung
    andersleung committed Aug 18, 2020
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  2. Merge branch 'master' into readsHtsgetDataSource

    @andersleung
    andersleung committed Aug 18, 2020
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Commits on Aug 19, 2020

  1. Add readme to htsgetScripts, move htsget_config.json

    @andersleung
    andersleung committed Aug 19, 2020
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  2. Remove ReadsHtsgetDataSource and GATK versions of htsget classes 

    * Switch to using htsjdk versions of htsget primitives
* Update unit tests
    @andersleung
    andersleung committed Aug 19, 2020
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