make blacklist argument optional

pinellolab · Nov 30, 2017 · 8626f42 · 8626f42
1 parent f9e05dd
commit 8626f42
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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',