Adding ADAM to SAM conversion. #250
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| //ERIC: Why does this take forever: |
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Ha, sorry. Let me clean that...
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| // build header | ||
| val header: SAMFileHeader = createSAMHeader(refDict, readGroups) |
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Is there a reason why we do this once per SAMRecord, rather than (first) collapsing all the ADAMRecords down into a SAMFileHeader and then passing that value in (calculated once) as an argument to this method?
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Ah yes, good point. I think we do things in backwards order here... I'll fix.
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@tdanford I've just updated to generate the header before we do the record conversion. I have also rebased, because, y'know. |
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| * Converts a single ADAM record into a SAM record. | ||
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| * @param adamRecord ADAM formatted alignment record to convert. | ||
| * @param dict Reference sequence dictionary to use for conversion. |
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This line (and the next one) are out of date.
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@fnothaft I just filed a PR to your feature branch, with (what I think is) a failing test... let me know if you think that's a valid test or not, though. |
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Thanks @tdanford; I believe your failing test is a valid test, and I will review and fix. |
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Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/340/ |
Adding a round-trip test which fails (at the moment) with an NPE -- I *think* this is related to the failure to write out the RG tags?
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@tdanford I've fixed the failing test, and have also cleaned up the other items you noted. |
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| import org.bdgenomics.adam.avro.ADAMRecord | ||
| import org.bdgenomics.adam.models.{ | ||
| Attribute, |
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| import org.bdgenomics.adam.rdd.ADAMContext._ | ||
| import org.scalatest.FunSuite | ||
| import scala.collection.JavaConverters._ |
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| package org.bdgenomics.adam.util | ||
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| import fi.tkk.ics.hadoop.bam.{ KeyIgnoringBAMOutputFormat, SAMFormat } |
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I'm going to just merge this as is and then followup with a pull request to clean up our import statements. |
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Thanks, Frank! |
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how to perform adam actions to convert from .adam file format to bam file. |
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@ankushreddy you'll want to do: |
This commit adds a conversion function for going from ADAM back to SAM or BAM. This work was done by @erictu; I've just gone ahead and rebased it on top of master, and done some small clean up. This resolves #49.