Merge branch 'tandem_tweaks_rebased' into 'dev'

better handling of abpoa errors

See merge request research/medaka!568

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - An issue with co-ordinate handling in computing variants from alignments.
 ### Added
 - Ability to use basecaller model name as --model argument.
+- Better handling or errors when running abpoa.
 
 ## [v1.11.0]
 ### Fixed

medaka/__init__.py

@@ -13,6 +13,12 @@
     sys.stderr.write(
         "Cannot import pyabpoa, some features may not be available.\n")
     abpoa = None
+try:
+    import wurlitzer
+except ImportError:
+    sys.stderr.write(
+        "Cannot import wurlitzer, some features may not be available.\n")
+    wurlitzer = None
 
 
 def check_minimap2_version():

medaka/medaka.py

@@ -531,10 +531,13 @@ def medaka_parser():
         help='Sample sex, required for appropriate handling of X/Y chromosomes including PAR regions.')
     trparser.add_argument('output', help='Output directory.')
     trparser.add_argument('--phasing', choices=set(medaka.tandem.phasing_options.keys()),
-        default='hybrid', help='Phasing method. prephased: '
-        'use HP bam tags. abpoa: abpoa diploid clustering. '
-        'hybrid: try prephased, use abpoa when either '
-        'haplotype has < --depth coverage.')
+        default='hybrid', help='Phasing method. '
+        'prephased: use HP bam tags. '
+        'abpoa: abpoa diploid clustering. '
+        'hybrid: try prephased, use abpoa when either haplotype has < --depth '
+        'coverage.'
+        'unphased: assume sample is haploid / homozygous in target regions.'
+    )
     trparser.add_argument('--depth', type=int, default=3,
         help='Minimum reads per haplotype.')
     trparser.add_argument('--min_mapq', type=int, default=5,