[MODIF] add support for .vcf.gz

Author: nservant

CHANGELOG

@@ -3,6 +3,8 @@ CHANGES IN VERSION 3.0.0
 
 NEW FEATURES
 
+  o vcf file can be zipped in vcf.gz
+
   o Add a Dockerfile for automatic Docker build on DockerHub
 
   o Set up Travis continuous testing
@@ -15,6 +17,8 @@ NEW FEATURES
 
 SIGNIFICANT USER-VISIBLE CHANGES
 
+  o SORT_RAM is not divided by N_CPU for samtools (#369)
+
   o Fix bug in make_viewpoints.py if multiple viewpoints are specified in the bed file
 
   o Add '--float' option for hicpro2higlass to manage normalized Hi-C data

doc/MANUAL.md

@@ -70,12 +70,12 @@ Copy and edit the configuration file *'config-hicpro.txt'* in your local folder.
 
 ----------------
 
-| ANNOTATION FILES      |                                                                                                                                   |
-|-----------------------|-----------------------------------------------------------------------------------------------------------------------------------|
-| REFERENCE_GENOME      | Reference genome prefix used for genome indexes. *Default: hg19*                                                                  |
-| GENOME_SIZE           | Chromsome size file. Loaded from the ANNOTATION folder in the HiC-Pro installation directory. *Default: chrom_hg19.sizes*         |
-| [CAPTURE_TARGET]      | BED file of target regions to focus on (mainly used for capture Hi-C data)                                                        |
-| [ALLELE_SPECIFIC_SNP] | VCF file to SNPs which can be used to distinguish parental origin. See the [allele specific section]( AS.md) for details   |
+| ANNOTATION FILES      |                                                                                                                                              |
+|-----------------------|----------------------------------------------------------------------------------------------------------------------------------------------|
+| REFERENCE_GENOME      | Reference genome prefix used for genome indexes. *Default: hg19*                                                                             |
+| GENOME_SIZE           | Chromsome size file. Loaded from the ANNOTATION folder in the HiC-Pro installation directory. *Default: chrom_hg19.sizes*                    |
+| [CAPTURE_TARGET]      | BED file of target regions to focus on (mainly used for capture Hi-C data)                                                                   |
+| [ALLELE_SPECIFIC_SNP] | VCF file (.vcf or .vcf.gz) to SNPs which can be used to distinguish parental origin. See the [allele specific section]( AS.md) for details   |
 
 ----------------
 

scripts/markAllelicStatus.py

@@ -17,7 +17,7 @@
 import os
 import re
 import pysam
-
+import gzip
 
 def usage():
     """Usage function"""
@@ -93,7 +93,10 @@ def load_vcf(in_file, filter_qual=False, verbose=False, debug=False):
     if verbose:
         print("## Loading VCF file {} ...".format(in_file))
 
-    vcf_handle = open(in_file)    
+    if ".gz" in in_file:
+        vcf_handle = gzip.open(in_file, 'r')
+    else:
+        vcf_handle = open(in_file)    
     header = []
     samples = []
     snps = {}