Commits

Davide Cittaro committed f7dceca

sorted samples in breakdancer vcf

Comments (0)

Files changed (1)

breakdancer2vcf.py

   options.output.write('##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n')
   options.output.write('##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of reads supporting the SV in this sample">\n')
   options.output.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT")
-  for library in bd_info['lib_info'].keys():
+  samples = bd_info['lib_info'].keys()
+  samples.sort()
+  for library in samples:
     options.output.write("\t%s" % os.path.basename(library))
   options.output.write('\n')  
 
   
   # process lines
   samples = bd_info['lib_info'].keys()
+  samples.sort()
   for record in cli_options.input:
     sv = SV_variant(record, genome)
     cli_options.output.write(sv.build_vcf_string(samples))