[partition] Sort reads by name

tanghaibao · Nov 23, 2017 · 06200c0 · 06200c0
1 parent f0ffa16
commit 06200c0
Showing 1 changed file with 11 additions and 2 deletions.
diff --git a/hic/partition.nim b/hic/partition.nim
@@ -9,6 +9,7 @@
 #
 
 
+import algorithm
 import hts
 import logging
 
@@ -18,6 +19,7 @@ logger.addHandler()
 type
   Partitioner* = ref object
     bamfile*: string
+  ReadMapping* = tuple[name: string, contig: string]
 
 
 proc initPartitioner*(bamfile: string): Partitioner =
@@ -29,6 +31,13 @@ proc count_links*(this: Partitioner) =
   var b: Bam
   open(b, this.bamfile, index=false)
 
+  var mappings: seq[ReadMapping] = @[]
+
   for record in b:
-    echo record
-    break
+    mappings.add((record.qname, record.chrom))
+
+  mappings.sort do (x, y: ReadMapping) -> int:
+    result = cmp(x.name, y.name)
+
+  for mapping in mappings[0..<100]:
+    echo mapping