Do not read contig and filter header lines on VCF ingest #189
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Signed-off-by: Karen Feng <[email protected]>
henrydavidge
approved these changes
Apr 14, 2020
| headers.flatMap { header => | ||
| val infoHeaderLines = header.getInfoHeaderLines.asScala | ||
| val formatHeaderLines = header.getFormatHeaderLines.asScala | ||
| val contigHeaderLines = header.getContigLines.asScala | ||
| val filterHeaderLines = header.getFilterLines.asScala | ||
| val contigHeaderLines = |
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nit: can you consolidate into a single if else? Generally it's less error-prone to check flags in as few places as possible.
| @@ -103,19 +103,23 @@ object VCFHeaderUtils extends GlowLogging { | |||
| } | |||
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| /** | |||
| * Find the unique header lines from an RDD of VCF headers. | |||
| * Find the unique desired header lines from an RDD of VCF headers. | |||
| * If lines of the same class found with the same ID, we pick one unless they are incompatible. | |||
| * If there are incompatible lines, [[IllegalArgumentException]] is thrown. | |||
| * Incompatible lines are: | |||
| * - FORMAT or INFO lines with the same ID but different types or counts | |||
| * - contig lines with the same ID but different lengths | |||
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Add a brief comment about the meaning of getNonSchemaHeaderLines.
Codecov Report
@@ Coverage Diff @@
## master #189 +/- ##
==========================================
- Coverage 93.67% 93.64% -0.03%
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Files 86 86
Lines 4077 4077
Branches 379 365 -14
==========================================
- Hits 3819 3818 -1
- Misses 258 259 +1
Continue to review full report at Codecov.
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Signed-off-by: Karen Feng <[email protected]>
henrydavidge
pushed a commit
to henrydavidge/glow
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Jun 22, 2020
…#189) * Do not read contig and filter header lines on VCF ingest Signed-off-by: Karen Feng <[email protected]> * Cleanup Signed-off-by: Karen Feng <[email protected]> Signed-off-by: Henry Davidge <[email protected]>
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What changes are proposed in this pull request?
With #173, VCF ingest now fails when merging files with contig lines that are missing the
lengthfield. This is resolved in newer versions of the HTSJDK as of samtools/htsjdk#1418.As we don't need contig and filter header lines for schema inference during VCF ingest, we can skip reading them entirely. This PR adds an option to skip reading non-schema header lines while reading unique header lines.
How is this patch tested?