fix: refget-compat checksums must use uppercase contig seq

bento-platform · Dec 22, 2023 · 247c5d2 · 247c5d2
1 parent 904699b
commit 247c5d2
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/fasta_checksum_utils/_contig.py b/fasta_checksum_utils/_contig.py
@@ -21,6 +21,7 @@ def gen_sequence() -> Generator[bytes, None, None]:
             yield (
                 fh
                 .fetch(contig_name, offset, min(offset + SEQUENCE_CHUNK_SIZE, contig_length))
+                .upper()  # See http://samtools.github.io/hts-specs/refget.html#checksum-calculation
                 .encode("ascii")
             )