refactored the parameter interface

Author: terhorst

conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: smcpp
-  version: {{ GIT_DESCRIBE_TAG.lstrip("v") }}
+  version: {{ environ['GIT_DESCRIBE_TAG'].lstrip("v") }}
 
 source:
   git_url: ../

conda/run_test.sh

@@ -4,7 +4,7 @@ set -e
 $SMC vcf2smc -v example/example.vcf.gz /tmp/example.1.smc.gz 1 msp1:msp_0,msp_1,msp_2
 $SMC vcf2smc -d msp_0 msp_0 example/example.vcf.gz /tmp/example.2.smc.gz 1 msp2:msp_0,msp_3,msp_4
 $SMC vcf2smc -d msp_1 msp_1 example/example.vcf.gz /tmp/example.12.smc.gz 1 msp1:msp_1,msp_2 msp2:msp_3,msp_4,msp_0
-$SMC estimate -o /tmp/out/1 --unfold --knots 5 --no-multi --em-iterations 1 1.25e-8 /tmp/example.1.smc.gz
+$SMC estimate -o /tmp/out/1 --unfold --knots 5 --em-iterations 1 1.25e-8 /tmp/example.1.smc.gz
 $SMC estimate -p 0.01 -r 1e-8 -o /tmp/out/2 --knots 5 --em-iterations 1 1.25e-8 /tmp/example.2.smc.gz
 $SMC split -o /tmp/out/split --em-iterations 1 \
     /tmp/out/1/model.final.json \

smcpp/commands/vcf2smc.py

@@ -158,10 +158,11 @@ def rec2gt(rec):
                 ref = rec.alleles[0]
                 for di in dist:
                     for d, i in di:
-                        if len(rec.samples[d]) != 2:
+                        if len(rec.samples[d].alleles) != 2:
                             raise RuntimeError(
                                 "Expected a diploid genotype at position {} "
-                                "for individual {} but found:\n{}".format(rec.pos, d, rec))
+                                "for individual {} but found:\n{}".format(rec.pos, d,
+                                    list(rec.samples[d].alleles)))
                 da = [[rec.samples[d].alleles[i]
                    for d, i in di] for di in dist]
                 a = [sum([x != ref for x in d])