Upgrade Hadoop BAM for better interval filtering

hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

Apache License 2.0

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Upgrade Hadoop BAM for better interval filtering #569

Closed arahuja closed 7 years ago

arahuja commented 7 years ago

This brings back #433 and fixes #399

@ryan-williams I think you tested switching the Java version on a single Spark submission, can we add something to the README on that? This PR will move the repository to Java 8 only

This change is

coveralls commented 7 years ago

Coverage increased (+0.04%) to 75.235% when pulling 1fa0b10dc66cbd9daebaa983a28b12e270065d8c on hbupgrade into e3c276d86c79630dbbc8a99939ad12f8817fb3b6 on master.

ryan-williams commented 7 years ago

OK, sorry for the delay here @arahuja, this lgtm.

I just sent #578 that resolves the conflicts here and adds a couple of things.

I am agnostic about whether you incorporate any/all of it or just rebase this and merge it in yourself.

Lmk if you have any questions about what I'd proposed over on #578.

coveralls commented 7 years ago

Coverage decreased (-0.03%) to 78.543% when pulling d297189a677dcaf77043e669fc4440fee095079c on hbupgrade into a6771eeafed073e6858979e01b214b214d965a1f on master.

coveralls commented 7 years ago

Coverage increased (+0.04%) to 78.609% when pulling 9399060619e5f4f9890636f8bec3affb553c42c3 on hbupgrade into a6771eeafed073e6858979e01b214b214d965a1f on master.

arahuja commented 7 years ago

I re-based this PR, and then added your commit on top.

I added one more commit to change a matching on Option to be a fold instead as I think matching on Option is not recommended.

I similarly changed a for on option to foreach.

ryan-williams commented 7 years ago

Sounds good.

matching on Option is not recommended.

Interesting; any reason?

arahuja commented 7 years ago

Interesting; any reason?

Just boilerplate already built-in to map, fold or foreach