From 8626f42793ed97ee7aec52682b8749aa23eb032f Mon Sep 17 00:00:00 2001 From: Rick Farouni Date: Thu, 30 Nov 2017 11:40:41 -0500 Subject: [PATCH] make blacklist argument optional --- haystack/find_hotspots.py | 2 +- haystack/run_pipeline.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/haystack/find_hotspots.py b/haystack/find_hotspots.py index 805fdbb7..b7f4ab00 100755 --- a/haystack/find_hotspots.py +++ b/haystack/find_hotspots.py @@ -252,7 +252,7 @@ def create_tiled_genome(genome_name, sb.call(cmd, shell=True) - if blacklist=='': + if blacklist == 'none': info('Tiled genome file created will not be blacklist filtered') else: diff --git a/haystack/run_pipeline.py b/haystack/run_pipeline.py index 1d2d4c1b..81c43507 100755 --- a/haystack/run_pipeline.py +++ b/haystack/run_pipeline.py @@ -82,7 +82,7 @@ def get_args_pipeline(): help='Exclude blacklisted regions. Blacklisted regions are not excluded by default. ' 'Use hg19 to blacklist regions for the human genome 19, ' 'otherwise provide the filepath for a bed file with blacklisted regions.', - default='') + default='none') parser.add_argument('--chrom_exclude', type=str, help='Exclude chromosomes that contain given (regex) string. For example _random|chrX|chrY excludes random, X, and Y chromosome regions',