revert sort_vcf logic

preprocess/SortVcf.py

@@ -171,57 +171,62 @@ def sort_vcf_from(args):
     else:
         output = open(output_fn, 'w')
 
-    contig_dict = defaultdict(str)
-    for vcf_fn in all_files:
-        file = os.path.join(input_dir, vcf_fn)
-        if is_lz4_format:
-            read_proc = subprocess_popen(shlex.split("{} {}".format("lz4 -fdc", file)), stderr=subprocess.DEVNULL)
-            fn = read_proc.stdout
-        else:
-            fn = open(file, 'r')
-        for row in fn:
-            row_count += 1
-            if row[0] == '#':
-                # skip phasing command line only occur with --enable_phasing, otherwise would lead to hap.py evaluation failure
-                if row.startswith('##commandline='):
+    for contig in contigs_order_list:
+        contig_dict = defaultdict(str)
+        contig_vcf_fns = [fn for fn in all_files if contig in fn]
+        for vcf_fn in contig_vcf_fns:
+            file = os.path.join(input_dir, vcf_fn)
+            if is_lz4_format:
+                read_proc = subprocess_popen(shlex.split("{} {}".format("lz4 -fdc", file)), stderr=subprocess.DEVNULL)
+                fn = read_proc.stdout
+            else:
+                fn = open(file, 'r')
+            for row in fn:
+                row_count += 1
+                if row[0] == '#':
+                    # skip phasing command line only occur with --enable_phasing, otherwise would lead to hap.py evaluation failure
+                    if row.startswith('##commandline='):
+                        continue
+                    if row not in header:
+                        header.append(row)
                     continue
-                if row not in header:
-                    header.append(row)
-                continue
-            # use the first vcf header
-            columns = row.strip().split(maxsplit=3)
-            ctg_name, pos = columns[0], columns[1]
-            contig_dict[(ctg_name, int(pos))] = row
-            no_vcf_output = False
-        fn.close()
-        if is_lz4_format:
-            read_proc.wait()
-    if need_write_header and len(header):
-        #add cmdline for gvcf
-        if "##cmdline" not in '\n'.join(header) and os.path.exists(cmd_fn):
-            cmdline_str = ""
-            if cmd_fn is not None and os.path.exists(cmd_fn):
-                cmd_line = open(cmd_fn).read().rstrip()
-
-                if cmd_line is not None and len(cmd_line) > 0:
-                    cmdline_str = "##cmdline={}\n".format(cmd_line)
-            if cmdline_str != "":
-                insert_index = 3 if len(header) >= 3 else len(header) - 1
-                header.insert(insert_index, cmdline_str)
-
-        if output_bgzip_gvcf:
-            header = check_header_in_gvcf(header=header, contigs_list=all_contigs_list)
-        output.write(''.join(header))
-        need_write_header = False
-    all_pos = sorted(contig_dict.keys(), key=lambda x: (contigs_order_list.index(x[0]), x[1]))
-    for pos in all_pos:
-        if args.pileup_only:
-            row = contig_dict[pos]
-            row = postprocess_row_with_params(args, row)
-            if row is not None:
+                # use the first vcf header
+                columns = row.strip().split(maxsplit=3)
+                ctg_name, pos = columns[0], columns[1]
+                # skip vcf file sharing same contig prefix, ie, chr1 and chr11
+                if ctg_name != contig:
+                    break
+                contig_dict[int(pos)] = row
+                no_vcf_output = False
+            fn.close()
+            if is_lz4_format:
+                read_proc.wait()
+        if need_write_header and len(header):
+            #add cmdline for gvcf
+            if "##cmdline" not in '\n'.join(header) and os.path.exists(cmd_fn):
+                cmdline_str = ""
+                if cmd_fn is not None and os.path.exists(cmd_fn):
+                    cmd_line = open(cmd_fn).read().rstrip()
+
+                    if cmd_line is not None and len(cmd_line) > 0:
+                        cmdline_str = "##cmdline={}\n".format(cmd_line)
+                if cmdline_str != "":
+                    insert_index = 3 if len(header) >= 3 else len(header) - 1
+                    header.insert(insert_index, cmdline_str)
+
+            if output_bgzip_gvcf:
+                header = check_header_in_gvcf(header=header, contigs_list=all_contigs_list)
+            output.write(''.join(header))
+            need_write_header = False
+        all_pos = sorted(contig_dict.keys())
+        for pos in all_pos:
+            if args.pileup_only:
+                row = contig_dict[pos]
+                row = postprocess_row_with_params(args, row)
+                if row is not None:
+                    output.write(contig_dict[pos])
+            else:
                 output.write(contig_dict[pos])
-        else:
-            output.write(contig_dict[pos])
 
     if compress_gvcf_output:
         write_proc.stdin.close()