Annotation Sprint 2 Task List

[cristinaetrv]

Background:

Improving Annotation for Maintainability

Completion Criteria:

hg19 and hg38 database that has exact match for dbSNP and ClinVar, add back 'intergenic'

Implementation Summary

• Switch from using dbSNP tab separated to VCF file for exact match (tab separated gives no guarantee that allelic representation matches)
• Switch from using ClinVar tab separated to VCF file for exact match (tab separated gives no guarantee that allelic representation matches)
• Ensure global regex's are applied to values being inserted into the database
  - Every track will have to ensure that it applies the replacement method which will be defined in class Tracks::build
  - Document this
• Replace unit separator with forward slash
• Write replacement unit tests for overlapping values

[akotlar]

See #304 and #300 for dbSNP 2 - related PRs.

I've tested building the resulting transformed file (100k lines), and that works well. For instance, querying chr1:10114, shows us the expected data, see attached

Expected features (these will be displayed in order, from index 0 to index 10 in the next image):

The result in Bystro

The expected allele frequencies, per population

[akotlar]

"Write replacement unit tests for overlapping values" is already done, see:

• bystro/perl/t/tracks/gene/overlap.t

  Line 29 in 9d64609

  PrepareConfigWithTempdirs( 't/tracks/gene/overlap.yml',

• bystro/perl/t/tracks/sparse/build_clinvar.t

  Line 65 in 9d64609

  # We expect an overlap, first the indel, then the snp

• bystro/perl/t/tracks/nearest/integration.t

  Line 36 in 9d64609

  # such as calculating the maximum range of the overlap: in previous code iterations

• bystro/perl/t/tracks/gene/join.t

  Line 38 in 9d64609

  # such as calculating the maximum range of the overlap: in previous code iterations

• https://github.com/bystrogenomics/bystro/blob/9d64609c44942f30ce7a21a1c4fd6d996fc808e9/perl/t/tracks/merge.t

"Write replacement unit tests for overlapping values" and "Ensure global regexes applied" is done, see:

• code: https://github.com/bystrogenomics/bystro/blob/master/perl/lib/Seq/Tracks/Build.pm#L199, which is applied by every track except CADD and Score, which deal only with numeric values: https://github.com/search?q=repo%3Abystrogenomics%2Fbystro%20coerceFeatureType&type=code

• tests: https://github.com/bystrogenomics/bystro/blob/master/perl/t/output/delimiters.t,

  bystro/perl/t/tracks/build/coerceFeatureType.t

  Line 33 in 9d64609

  my $res = $seq->coerceFeatureType( 'someString', $str );

[cristinaetrv]

Remaining work moved to Sprint 3