Minor fixes and inputs checks

- Version flag now gets correct package version
- Sample more reads when checking for consistent
  reads sizes
- Check for overlap between SV chroms and CNVs
  intended to make errors clearer, see
  #25

SVclone/SVprocess/bamtools.py

@@ -85,7 +85,7 @@ def estimateInsertSizeDistribution(bamfile,
 
 
 def estimateTagSize(bamfile,
-                    alignments=10,
+                    alignments=1000,
                     multiple="error"):
     '''estimate tag size from first alignments in file.'''
     samfile = pysam.AlignmentFile(bamfile)

SVclone/cli.py

@@ -12,12 +12,13 @@
 
 import argparse
 import numpy as np
+import pkg_resources
 
 def main():
 
 	parser = argparse.ArgumentParser(prog='SVclone')
 
-	parser.add_argument('--version', action='version', version='SVclone-1.0.2')
+	parser.add_argument('--version', action='version', version=pkg_resources.get_distribution("SVclone").version)
 
 	subparsers = parser.add_subparsers()
 

SVclone/run_filter.py

@@ -332,6 +332,13 @@ def match_copy_numbers(var_df, cnv_df, strict_cnv_filt, sv_offset, bp_fields=['c
     bp_chroms = np.unique(var_df[chrom_field].values)
     bp_chroms = natural_sort(bp_chroms)
 
+    bp_chrom_overlap = [bchr in cnv_df['chr'].values for bchr in bp_chroms]
+    if not np.any(bp_chrom_overlap):
+        raise ValueError('''
+No SV chroms match the CNV input!
+Check that your chromosome names are compatible.
+              ''')
+
     adj_cnv_field   = '%s_adjacent' % gtype_field
     cnv_dist_field  = '%s_cnv_boundary_dist' % gtype_field
 

setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 setup(name='SVclone',
-      version='v1.1.0',
+      version='v1.1.3',
       description='A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.',
       url='https://github.com/mcmero/SVclone',
       author='Marek Cmero',