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Add utility methods for adam-shell #1958

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merged 1 commit into from Mar 23, 2018

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heuermh commented Mar 21, 2018

E.g.

scala> import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.ADAMContext._

scala> import org.bdgenomics.adam.util.ADAMShell._
import org.bdgenomics.adam.util.ADAMShell._

scala> val variants = sc.loadVariants("Mills_and_1000G_gold_standard.indels.variants.adam")
variants: org.bdgenomics.adam.rdd.variant.VariantRDD = ParquetUnboundVariantRDD with 3366 reference sequences

scala> printVariantFilters(variants)
Filter Header Lines
FILTER=<ID=PASS,Description="Truth sensitivity tranche level at VQS Lod < -381.3592">

Variant Filters
+-------------+--------+--------+-------+--------+-----------------+----------------+----------------+
| Contig Name | Start  |  End   |  Ref  |  Alt   | Filters Applied | Filters Passed | Filters Failed |
+-------------+--------+--------+-------+--------+-----------------+----------------+----------------+
|        chr1 |  55248 |  55249 | C     | CTATGG |            true |           true |             [] |
|        chr1 |  87113 |  87115 | CT    | C      |            true |           true |             [] |
|        chr1 | 263834 | 263837 | CCT   | C      |            true |           true |             [] |
|        chr1 | 756186 | 756191 | CACAG | C      |            true |           true |             [] |
|        chr1 | 779928 | 779930 | AG    | A      |            true |           true |             [] |
|        chr1 | 786693 | 786694 | A     | ATT    |            true |           true |             [] |
|        chr1 | 796753 | 796754 | T     | TA     |            true |           true |             [] |
|        chr1 | 816926 | 816928 | AT    | A      |            true |           true |             [] |
|        chr1 | 822795 | 822798 | CCT   | C      |            true |           true |             [] |
|        chr1 | 824063 | 824068 | ATATT | A      |            true |           true |             [] |
+-------------+--------+--------+-------+--------+-----------------+----------------+----------------+
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AmplabJenkins commented Mar 21, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2732/
Test PASSed.

@fnothaft

Nice! This is a great idea! Did you want to add to this, or would you be OK with me merging this into 0.24.0?

@heuermh

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heuermh commented Mar 21, 2018

Did you want to add to this, or would you be OK with me merging this into 0.24.0?

There is probably more to add, but if you think the pattern is right, then merging into 0.24.0 is ok with me. I'll squash into one commit.

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AmplabJenkins commented Mar 21, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2733/
Test PASSed.

@fnothaft fnothaft merged commit b86c4ad into bigdatagenomics:master Mar 23, 2018

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Codacy/PR Quality Review Not so good... This pull request quality could be better.
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fnothaft commented Mar 23, 2018

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:adam-shell-utils branch Mar 23, 2018

@heuermh heuermh added this to the 0.24.0 milestone Mar 23, 2018

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