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Complain if both --write-index and --naive options are given
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pd3 committed Jan 31, 2024
1 parent c492f03 commit f33fd1d
Showing 1 changed file with 1 addition and 0 deletions.
1 change: 1 addition & 0 deletions vcfconcat.c
Original file line number Diff line number Diff line change
Expand Up @@ -1107,6 +1107,7 @@ int main_vcfconcat(int argc, char *argv[])
if ( args->regions_list && !args->allow_overlaps ) error("The -r/-R option is supported only with -a\n");
if ( args->naive_concat )
{
if ( args->write_index ) error("Error: cannot --write-index in the %s mode\n",args->naive_concat_trust_headers?"--naive-force":"--naive");
if ( args->allow_overlaps ) error("The option --naive cannot be combined with --allow-overlaps\n");
if ( args->phased_concat ) error("The option --naive cannot be combined with --ligate\n");
if ( args->sites_only ) error("The option --naive cannot be combined with --drop-genotypes\n");
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