From 608baf7fed564ba2dd151cc1fbdd580f001f816b Mon Sep 17 00:00:00 2001 From: kathryn1995 Date: Fri, 2 Oct 2026 22:00:40 -0700 Subject: [PATCH] Clarify pseudocigar_chrom_col docs when no full location is set --- src/pmotools/pmo_builder/mhap_table_to_pmo.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/pmotools/pmo_builder/mhap_table_to_pmo.py b/src/pmotools/pmo_builder/mhap_table_to_pmo.py index fb00da7..32f0916 100644 --- a/src/pmotools/pmo_builder/mhap_table_to_pmo.py +++ b/src/pmotools/pmo_builder/mhap_table_to_pmo.py @@ -80,7 +80,7 @@ def mhap_table_to_pmo( :type microhaplotype_name_col: str, optional :param pseudocigar_col: the name of the column containing a pseudocigar for the microhaplotype :type pseudocigar_col: str, optional - :param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col + :param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col. chrom_col can only be set together with start_col and end_col, so use pseudocigar_chrom_col when there is no full microhaplotype location :type pseudocigar_chrom_col: str, optional :param pseudocigar_start_col: column for the pseudocigar ref_loc start (required if pseudocigar_col is set) :type pseudocigar_start_col: str, optional @@ -233,7 +233,7 @@ def create_representative_microhaplotype_dict( :type microhaplotype_name_col: str, optional :param pseudocigar_col: the name of the column containing a pseudocigar for the microhaplotype :type pseudocigar_col: str, optional - :param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col + :param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col. chrom_col can only be set together with start_col and end_col, so use pseudocigar_chrom_col when there is no full microhaplotype location :type pseudocigar_chrom_col: str, optional :param pseudocigar_start_col: column for the pseudocigar ref_loc start (required if pseudocigar_col is set) :type pseudocigar_start_col: str, optional @@ -273,8 +273,9 @@ def create_representative_microhaplotype_dict( ): raise ValueError( "pseudocigar_col is set, so a Pseudocigar ref_loc must be " - "constructable: set a chromosome (pseudocigar_chrom_col or " - "chrom_col), pseudocigar_start_col, and pseudocigar_end_col." + "constructable: set a chromosome (pseudocigar_chrom_col, or " + "chrom_col together with start_col and end_col), " + "pseudocigar_start_col, and pseudocigar_end_col." ) def get_if_present(row, col):