# HG changeset patch
# User nicksto <nmapsy@gmail.com>
# Date 1449677013 18000
# Node ID e5d39283fe4d7b2c2c2817dde21d5df0bb2991b7
# Parent  df1fb577db0d3b66bf5b6c0aab7be24ed217b66f
allele-counts.py: Document output columns.

diff -r df1fb577db0d -r e5d39283fe4d allele-counts.py
--- a/allele-counts.py	Tue Dec 03 13:45:16 2013 -0500
+++ b/allele-counts.py	Wed Dec 09 11:03:33 2015 -0500
@@ -23,8 +23,8 @@
 COLUMN_LABELS = ['SAMPLE', 'CHR',  'POS', 'A', 'C', 'G', 'T', 'CVRG', 'ALLELES',
   'MAJOR', 'MINOR', 'MAF', 'BIAS']
 CANONICAL_VARIANTS = ['A', 'C', 'G', 'T']
-USAGE = """Usage: %prog [options] -i variants.vcf -o alleles.csv
-       cat variants.vcf | %prog [options] > alleles.csv"""
+USAGE = """Usage: %prog [options] -i variants.vcf -o alleles.tsv
+       cat variants.vcf | %prog [options] > alleles.tsv"""
 OPT_DEFAULTS = {'infile':'-', 'outfile':'-', 'freq_thres':1.0, 'covg_thres':100,
   'print_header':False, 'stdin':False, 'stranded':False, 'no_filter':False,
   'debug_loc':'', 'seed':''}
@@ -33,7 +33,15 @@
 number of reads of each base, determines the major allele, minor allele (second
 most frequent variant), and number of alleles above a threshold. So currently
 it only considers SNVs (ACGT), including in the coverage figure. By default it
-reads from stdin and prints to stdout."""
+reads from stdin and prints to stdout.
+Prints a tab-delimited set of statistics to stdout.
+To print output column labels, run "$ echo -n | ./allele-counts.py -H".
+The columns are: 1:SAMPLE 2:CHR 3:POS 4:A 5:C 6:G 7:T 8:CVRG 9:ALLELES 10:MAJOR
+11:MINOR 12:MAF 13:BIAS,
+unless the --stranded option is used, in which case they are:
+1:SAMPLE 2:CHR 3:POS 4:+A 5:+C 6:+G 7:+T 8:-A 9:-C 10:-G 11:-T 12:CVRG
+13:ALLELES 14:MAJOR 15:MINOR 16:MAF 17:BIAS.
+"""
 EPILOG = """Requirements:
 The input VCF must report the variants for each strand.
 The variants should be case-sensitive (e.g. all capital base letters).