From 6f49dd9b79636751a393167ce2a582bc8a3d2f17 Mon Sep 17 00:00:00 2001 From: Colin Gross Date: Tue, 10 Oct 2023 11:25:59 -0400 Subject: [PATCH] Correct call as get_sequences_info not yet moved to base class. --- bravo_api/VERSION | 2 +- bravo_api/core/s3_cram_source.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bravo_api/VERSION b/bravo_api/VERSION index 94f15e9..0e83a9a 100644 --- a/bravo_api/VERSION +++ b/bravo_api/VERSION @@ -1 +1 @@ -2.13.1 +2.13.2 diff --git a/bravo_api/core/s3_cram_source.py b/bravo_api/core/s3_cram_source.py index 8bf5dff..087606b 100644 --- a/bravo_api/core/s3_cram_source.py +++ b/bravo_api/core/s3_cram_source.py @@ -60,7 +60,7 @@ def get_info(self, variant_id): if chrom not in self.contigs: return [] else: - return CramSource.get_sequences_info(self.variant_map, chrom, int(pos), ref, alt) + return S3CramSource.get_sequences_info(self.variant_map, chrom, int(pos), ref, alt) def get_crai(self, variant_id, sample_no: int, sample_het: bool) -> io.BytesIO: """ Crai for data of individual sample that is representative of given variant @@ -75,7 +75,7 @@ def get_crai(self, variant_id, sample_no: int, sample_het: bool) -> io.BytesIO: chrom = CramSource.normalize_contig_prefix(chrom, self.contigs_chr_prefixed) sample_id = CramSource.lookup_sample_id(self.variant_map, chrom, pos, ref, alt, - sample_het, sample_no) + sample_het, sample_no) logger.debug('sample_id: %s', sample_id) cram_url = self.calc_cram_url(sample_id) @@ -100,7 +100,7 @@ def get_cram(self, variant_id: str, sample_no: int, sample_het: bool, # Lookup sample_id sample_id = CramSource.lookup_sample_id(self.variant_map, chrom, pos, ref, alt, - sample_het, sample_no) + sample_het, sample_no) # Lookup cram_path cram_url = self.calc_cram_url(sample_id)