CramSource get_info should return single dict instead of list with only one dict in it.

[grosscol]

Issue or current state

The get_info method of the legacy sequences hander returned a list with a single dictionary in it. The CramSource class mirrors this behavior to keep the API the same.

Resolved when

Change made in CramSource and subclasses:

• return dictionary instead of list
• return empty dict when no matching variant is found in variant_map.

Corresponding issue made in Bravue project.

Note about Bravue

The relevant code in the UI is in src/components/Reads.vue. An issue will have to be filed there and the changes to the API reflected in the data processing on the UI side.

     .get(`${this.api}/variant/api/snv/cram/summary/${this.variant.variant_id}`)
      .then( response => {
        var result = response.data;
        if (result.data.length > 0) {
          var counts = result.data[0];
          this.counts.n_homs = counts.n_homozygous;
          this.counts.n_hets = counts.n_heterozygous;
        }

[grosscol]

Relevant function in api:

bravo_api/bravo_api/core/cram_source.py

Lines 79 to 88 in 56623a7

	def het_hom_counts(tabix_file, chrom, pos, ref, alt):
	result = []
	for row in tabix_file.fetch(chrom, pos - 1, pos):
	if int(row[1]) == pos and row[2] == ref and row[3] == alt:
	result.append({
	'n_homozygous': len(row[4].split(',')) if row[4] else 0,
	'n_heterozygous': len(row[5].split(',')) if row[5] else 0
	})
	break
	return result

called from:

bravo_api/bravo_api/core/fs_cram_source.py

Lines 175 to 177 in 56623a7

	def get_sequences_info(variant_map, chrom, pos, ref, alt):
	with pysam.TabixFile(str(variant_map), parser=pysam.asTuple()) as itabix:
	return FSCramSource.het_hom_counts(itabix, chrom, pos, ref, alt)