index-anno fails with "error: stoi" on 5-column annotation file when variant ID has chr prefix (v0.11.1) #6
Description
Using a 5-column annotation file as described in the v0.9.0 release notes (numeric chrom in col4, integer pos in col5). The file is valid bgzip and tabix indexing with -s 4 -b 5 -e 5 succeeds, but index-anno consistently crashes with "error: stoi" when variant IDs in col1 have a chr prefix (e.g. chr22:12345:A:G).
As a workaround I am using the .tbi index from tabix directly — will this be accepted by the meta-analysis commands, or is the .idx format from index-anno required? I am using the .tbi index from tabix directly, but would appreciate a fix so that index-anno correctly handles the 5-column format regardless of the variant ID format in col1.