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Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests #832

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Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests #832

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@kstromhaug kstromhaug commented Apr 25, 2022 •
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Remove VariantContexts from HapCutToVcf and tests

kstromhaug
kstromhaug commented Apr 28, 2022
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src/main/scala/com/fulcrumgenomics/vcf/HapCutToVcf.scala
@@ -240,51 +207,51 @@ trait HeaderLines {
object HapCut1VcfHeaderLines extends HeaderLines {
val ReadCountFormatTag = "RC"
val ReadCountFormatDescription = "Counts of calls supporting allele0 and allele1 respectively"
val ReadCountFormatHeaderLine = new VCFFormatHeaderLine(ReadCountFormatTag, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, ReadCountFormatDescription)
val ReadCountFormatHeaderLine = VcfFormatHeader(ReadCountFormatTag, VcfCount.OnePerAltAllele, VcfFieldType.Integer, ReadCountFormatDescription)
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I think VCFHeaderLineCount.R == VcfCount.OnePerAllele but I'm not positive

kstromhaug
kstromhaug commented Apr 28, 2022
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src/main/scala/com/fulcrumgenomics/vcf/HapCutToVcf.scala
val (sourceContext, sourceOffset) = sourceIterator.next()
if (!hapCutReader.hasNext) formatSourceContext(sourceContext)
val (sourceVariant, sourceOffset) = sourceIterator.next()
if (!hapCutReader.hasNext) formatSourceVariant(sourceVariant)
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I assume it's safe to rename this function since it's private

@kstromhaug kstromhaug force-pushed the ks_hapcuttovcf_ctxremoval branch from 1cd61b8 to 8a8379c Compare April 29, 2022 20:24
@kstromhaug kstromhaug changed the base branch from ks_remove_variantcontextsetbuilder to ks_rm_variant_contexts April 29, 2022 20:25
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codecov-commenter commented Apr 29, 2022 •
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Codecov Report

❗ No coverage uploaded for pull request base (ks_rm_variant_contexts@15310b2). Click here to learn what that means.
The diff coverage is n/a.

❗ Current head 1cd61b8 differs from pull request most recent head 8a8379c. Consider uploading reports for the commit 8a8379c to get more accurate results

@@                    Coverage Diff                    @@
##             ks_rm_variant_contexts     #832   +/-   ##
=========================================================
  Coverage                          ?   95.61%           
=========================================================
  Files                             ?      122           
  Lines                             ?     7068           
  Branches                          ?      491           
=========================================================
  Hits                              ?     6758           
  Misses                            ?      310           
  Partials                          ?        0
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@kstromhaug kstromhaug force-pushed the ks_rm_variant_contexts branch from c81cca1 to 10f997f Compare April 29, 2022 20:34
@kstromhaug kstromhaug force-pushed the ks_hapcuttovcf_ctxremoval branch from 8a8379c to f971838 Compare April 29, 2022 20:38
@kstromhaug kstromhaug marked this pull request as ready for review April 29, 2022 21:00
@kstromhaug kstromhaug requested a review from nh13 April 29, 2022 21:00
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