Merge pull request #223 from golobor/parse_refactor

Parse refactor

Author: golobor

pairtools/cli/parse.py

@@ -123,7 +123,7 @@
 @click.option(
     "--walks-policy",
     type=click.Choice(["mask", "5any", "5unique", "3any", "3unique", "all"]),
-    default="mask",
+    default="5unique",
     help="the policy for reporting unrescuable walks (reads containing more"
     " than one alignment on one or both sides, that can not be explained by a"
     " single ligation between two mappable DNA fragments)."

pairtools/lib/pairsam_format.py

@@ -100,6 +100,10 @@
     "dist_to_3",
     "seq",
     "mismatches",  # Format: "{ref_letter}:{mut_letter}:{phred}:{ref_position}:{read_position}"
+    "read_side",
+    "algn_idx",
+    "same_side_algn_count"
+    
 ]
 
 DTYPES_EXTRA_COLUMNS = {
@@ -115,4 +119,7 @@
     "dist_to_3": int,
     "seq": str,
     "mismatches": str,
+    "read_side": int,
+    "algn_idx": int,
+    "same_side_algn_count": int,
 }