[ADAM-353] Fixing issue with SAM/BAM/VCF header attachment when running distributed #354
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| } | ||
| protected val rgs = RecordGroupDictionary.fromSAMHeader(hdr) | ||
|
|
||
| // recreate header when requested to get around header not being serializable, |
There was a problem hiding this comment.
Ah, yes! Thanks @hammer!
|
I've added a commit here that fixes #351 as well; we weren't handing symbolic alleles correctly. I'm glad to move that into it's own PR if people would prefer, LMK. |
fnothaft
force-pushed
the
fix-distributed-legacy-output
branch
from
5afa75b
to
c588a34
Compare
fnothaft
force-pushed
the
fix-distributed-legacy-output
branch
from
c588a34
to
a6f04c4
Compare
|
Rebased on master. |
| @@ -24,7 +24,7 @@ | |||
| <spark.version>1.0.1</spark.version> | |||
| <parquet.version>1.4.3</parquet.version> | |||
| <!-- Edit the following line to configure the Hadoop (HDFS) version. --> | |||
| <hadoop.version>2.2.0</hadoop.version> | |||
| <hadoop.version>1.0.4</hadoop.version> | |||
There was a problem hiding this comment.
Ah, sorry, did that for testing on EC2. I'll move it back.
fnothaft
force-pushed
the
fix-distributed-legacy-output
branch
from
a6f04c4
to
8672534
Compare
|
Rebased, and fixed hadoop version issue. |
| assert(allele.isNonReference && !allele.isSymbolic) | ||
| val variant = createADAMVariant(vc, Some(allele.getBaseString)) | ||
| val genotypes = extractNonReferenceGenotypes(vc, variant, calling_annotations) | ||
| assert(allele.isNonReference, |
There was a problem hiding this comment.
Did you mean to drop the check if the allele is not symbolic?
There was a problem hiding this comment.
Yes; this causes the problem in #351 with structural variants. I've added bigdatagenomics/bdg-formats#27 and #358 which are necessary to cleanly fix issue #351.
massie
added a commit
that referenced
this pull request
Sep 2, 2014
[ADAM-353] Fixing issue with SAM/BAM/VCF header attachment when running distributed
|
Thanks, Frank! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes issue #353. Runs header attachment per partition; not the cleanest fix, but it'll do. Modifies the SAMHeaderWritable class; without this modification, I was running into serialization issues.
@ryan-williams Can you give this a shot on your end? I've tried this on EC2 and it seems to work OK but would like to confirm that it works OK for you before merging it.