Merge pull request #59 from gymrek-lab/test-simgenotype

minor cleanups to simgenotype output messages

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 \

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