[partition] Update matrix entries in contact matrix

allhic.nim

@@ -28,7 +28,6 @@ proc optimize_main() =
 
 proc partition_main() =
   var c = initPartitioner("tests/prunning.sub.bam")
-  echo c.bamfile
   c.count_links()
 
 

hic/base.nim

@@ -0,0 +1,8 @@
+import future
+import logging
+import strutils
+import "matrix"
+
+
+var logger = newConsoleLogger()
+logger.addHandler()

hic/clm.nim

@@ -1,15 +1,10 @@
-import future
 import math
 import os
 import parseutils
 import sets
 import strutils
 import tables
-import logging
-import "matrix"
-
-var logger = newConsoleLogger()
-logger.addHandler()
+include "base"
 
 
 ##
@@ -104,7 +99,7 @@ proc M*(this: CLMFile): Matrix[int] =
     N = this.N
     tig_to_idx = this.tig_to_idx
 
-  result = newMatrix[int](N, N)
+  result = zeros[int](N, N)
   for abt, links in this.contacts.pairs():
     let (at, bt) = abt
     if at notin tig_to_idx:

hic/partition.nim

@@ -11,15 +11,10 @@
 
 import algorithm
 import hts
-import logging
-import strutils
 import tables
-import "matrix"
+include "base"
 
 
-var logger = newConsoleLogger()
-logger.addHandler()
-
 type
   Partitioner* = ref object
     bamfile*: string
@@ -41,16 +36,23 @@ proc count_links*(this: Partitioner) =
   for t in b.hdr.targets:
     targets[t.name] = t
 
-  let N = targets.len
-  var M = newMatrix[int](N, N)
+  let N = max(lc[ x.tid | (x <- b.hdr.targets), int]) + 1
+  var M = zeros[int](N, N)
+  debug("Initiating matrix of size $# x $#".format(N, N))
+
   for record in b:
-    let qi = targets[record.chrom].tid
-    let mi = targets[record.mate_chrom].tid
-    echo qi, " & ", mi
+    var
+       qi = targets[record.chrom].tid
+       mi = targets[record.mate_chrom].tid
+
+    if qi > mi:
+      swap(qi, mi)
+
+    M[qi, mi] = M[qi, mi] + 1
     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
+    echo mapping

install.sh

@@ -2,9 +2,10 @@
 
 echo $(pwd)
 
-sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
-     curl  libssl-dev libtool autoconf automake libcurl4-openssl-dev
+#sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
+#     curl  libssl-dev libtool autoconf automake libcurl4-openssl-dev
 
+BRANCH=latest
 export base=$(pwd)
 if [ ! -x nim-$BRANCH/bin/nim ]; then
   git clone -b $BRANCH --depth 1 git://github.com/nim-lang/nim nim-$BRANCH/