From f021d3a6cedf56b74b1ec4c81f99f7c1d08ed459 Mon Sep 17 00:00:00 2001 From: Melissa Gymrek Date: Thu, 30 Jun 2022 14:20:43 -0700 Subject: [PATCH] minor cleanups to simgenotype output messages --- haptools/__main__.py | 3 ++- haptools/sim_genotype.py | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/haptools/__main__.py b/haptools/__main__.py index 5830b84c..f16d28ab 100644 --- a/haptools/__main__.py +++ b/haptools/__main__.py @@ -70,9 +70,10 @@ def simgenotype(invcf, sample_info, model, mapdir, out, popsize, seed, chroms): Simulate admixed genomes under a pre-defined model. Example: + haptools simgenotype \ --model ./tests/data/outvcf_gen.dat \ - --mapdir ./tests/map/ \ + --mapdir ./tests/data/map/ \ --chroms 1,2 \ --invcf ./tests/data/outvcf_test.vcf \ --sample_info ./tests/data/outvcf_info.tab \ diff --git a/haptools/sim_genotype.py b/haptools/sim_genotype.py index 4d14f8b1..03cc2329 100644 --- a/haptools/sim_genotype.py +++ b/haptools/sim_genotype.py @@ -34,6 +34,8 @@ def output_vcf(breakpoints, model_file, vcf_file, sampleinfo_file, out): output prefix """ + print(f"Outputting VCF file {vcf_file}") + # details to know # vcf file: how to handle samples and which sample is which haplotype block randomly choose out of current population types # need to go line by line of the vcf when creating the new vcf