Merge pull request #61 from J35P312/supp_vec

2.7.0

Author: J35P312

setup.py

@@ -19,7 +19,7 @@
     ext_modules = []
 
 setup(name='svdb',
-      version='2.6.4',
+      version='2.7.0',
       url="https://github.com/J35P312/SVDB",
       author="Jesper Eisfeldt",
       author_email="jesper.eisfeldt@scilifelab.se",

svdb/__main__.py

@@ -38,7 +38,7 @@ def make_query_calls (args, queries, keyword):
         query_module.main(args)
 
 def main():
-    version = "2.6.4"
+    version = "2.7.0"
     parser = argparse.ArgumentParser(
         """SVDB-{}, use the build module to construct databases, use the query module to query the database usign vcf files, or use the hist module to generate histograms""".format(version), add_help=False)
     parser.add_argument('--build', help="create a db",

svdb/merge_vcf_module.py

@@ -75,13 +75,17 @@ def print_header(vcf_list, vcf_dictionary, args, command_line):
         print(header["INFO"][entry].strip())
     del header["INFO"]
 
+    supp_vector_order=[]
     for vcf in vcf_dictionary:
         print("##INFO=<ID={}_INFO,Number=.,Type=String,Description=\"pipe separated list of all details in the INFO column of file {}\">".format(vcf_dictionary[vcf],vcf_dictionary[vcf]))
         print("##INFO=<ID={}_SAMPLE,Number=.,Type=String,Description=\"pipe separated list of all details in the SAMPLEs column of file {}\">".format(vcf_dictionary[vcf],vcf_dictionary[vcf]))
         print("##INFO=<ID={}_CHROM,Number=.,Type=String,Description=\"pipe separated list of all details in the CHROM column of file {}\">".format(vcf_dictionary[vcf],vcf_dictionary[vcf]))
         print("##INFO=<ID={}_POS,Number=.,Type=String,Description=\"pipe separated list of all details in the POS column of file {}\">".format(vcf_dictionary[vcf],vcf_dictionary[vcf]))
         print("##INFO=<ID={}_QUAL,Number=.,Type=String,Description=\"pipe separated list of all details in the QUAL column of file {}\">".format(vcf_dictionary[vcf],vcf_dictionary[vcf]))
         print("##INFO=<ID={}_FILTERS,Number=.,Type=String,Description=\"pipe separated list of all details in the FILTER column of file {}\">".format(vcf_dictionary[vcf],vcf_dictionary[vcf]))
+        supp_vector_order.append(vcf_dictionary[vcf])
+
+    print("##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description=\"Vector of supporting callers/files (order: {}).\">".format(" ".join(supp_vector_order) ))
 
     # print contigs according to the input order
     if reference != "":

svdb/merge_vcf_module_cython.py

@@ -357,6 +357,15 @@ def merge(variants, samples, sample_order, sample_print_order, priority_order, a
             if not args.notag:
                 line[7]+=";svdb_origin={}".format("|".join(callers))
 
+            sup_vec=[]
+            for c in sorted(priority_order):
+                if c in filters_tag:
+                    sup_vec.append("1") 
+                else:
+                    sup_vec.append("0") 
+
+            line[7]+=";SUPP_VEC={}".format("".join(sup_vec))
+
             to_be_printed[line[0]].append(line)
 
             analysed_variants.add(i)