Skip to content

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

Open
kstromhaug wants to merge 1 commit intoks_rm_variant_contextsfrom
ks_hapcuttovcf_ctxremoval
Open

Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests#832
kstromhaug wants to merge 1 commit intoks_rm_variant_contextsfrom
ks_hapcuttovcf_ctxremoval

Conversation

@kstromhaug
Copy link

@kstromhaug kstromhaug commented Apr 25, 2022 •
edited
Loading

Remove VariantContexts from HapCutToVcf and tests

kstromhaug
kstromhaug commented Apr 28, 2022
View reviewed changes
src/main/scala/com/fulcrumgenomics/vcf/HapCutToVcf.scala
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)
Copy link
Author

@kstromhaug kstromhaug Apr 28, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think VCFHeaderLineCount.R == VcfCount.OnePerAllele but I'm not positive

kstromhaug
kstromhaug commented Apr 28, 2022
View reviewed changes
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)
Copy link
Author

@kstromhaug kstromhaug Apr 28, 2022

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
@codecov-commenter
Copy link

codecov-commenter commented Apr 29, 2022 •
edited
Loading

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
Flag Coverage Δ
unittests 95.61% <0.00%> (?)

Flags with carried forward coverage won't be shown. Click here to find out more.

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 15310b2...8a8379c. Read the comment docs.

@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
@nh13 nh13 removed their request for review September 25, 2025 22:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

help wanted

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@kstromhaug @codecov-commenter @nh13