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Add Pipe API #1112

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fnothaft opened this Issue Aug 11, 2016 · 0 comments

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fnothaft commented Aug 11, 2016

We want an API that allows us to pipe data via a stream from ADAM into a legacy tool running under Spark. This will allow us to run legacy tools under ADAM.

  • Streaming support for BAM/SAM
  • Streaming support for FASTQ
  • Streaming support for VCF
  • Streaming support for feature formats

@fnothaft fnothaft added this to the 0.20.0 milestone Aug 11, 2016

@fnothaft fnothaft self-assigned this Aug 11, 2016

fnothaft added a commit to fnothaft/adam that referenced this issue Aug 12, 2016

[ADAM-1112] Add interface for piping commands.
Resolves #1112. Adds interfaces for piping SAM/BAM and VCF to subprocesses that
are run in parallel under Apache Spark.

@fnothaft fnothaft referenced this issue Aug 12, 2016

Merged

Add pipes API #1114

@heuermh heuermh modified the milestone: 0.20.0 Sep 7, 2016

@heuermh heuermh referenced this issue Sep 7, 2016

Closed

Release ADAM version 0.20.0 #1048

47 of 61 tasks complete

fnothaft added a commit to fnothaft/adam that referenced this issue Sep 15, 2016

[ADAM-1112] Add interface for piping commands.
Resolves #1112. Adds interfaces for piping SAM/BAM and VCF to subprocesses that
are run in parallel under Apache Spark.

fnothaft added a commit to fnothaft/adam that referenced this issue Sep 15, 2016

[ADAM-1112] Add interface for piping commands.
Resolves #1112. Adds interfaces for piping SAM/BAM and VCF to subprocesses that
are run in parallel under Apache Spark.

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 3, 2016

[ADAM-1112] Add interface for piping commands.
Resolves #1112. Adds interfaces for piping SAM/BAM and VCF to subprocesses that
are run in parallel under Apache Spark.

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 7, 2016

[ADAM-1112] Add interface for piping commands.
Resolves #1112. Adds interfaces for piping SAM/BAM and VCF to subprocesses that
are run in parallel under Apache Spark.

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 13, 2016

[ADAM-1112] Add interface for piping commands.
Resolves #1112. Adds interfaces for piping SAM/BAM and VCF to subprocesses that
are run in parallel under Apache Spark.

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 14, 2016

[ADAM-1112] Add interface for piping commands.
Resolves #1112. Adds interfaces for piping SAM/BAM and VCF to subprocesses that
are run in parallel under Apache Spark.

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 14, 2016

[ADAM-1112] Add interface for piping commands.
Resolves #1112. Adds interfaces for piping SAM/BAM and VCF to subprocesses that
are run in parallel under Apache Spark.

@heuermh heuermh closed this in babf5cf Oct 14, 2016

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