[allhic] Add hic/partition

allhic.nim

@@ -5,6 +5,7 @@
 
 import docopt
 import hic/clm
+import hic/partition
 import strutils
 import tables
 
@@ -25,11 +26,16 @@ proc optimize_main() =
   c.parse()
 
 
+proc partition_main() =
+  var c = initPartitioner("tests/prunning.sub.bam")
+  echo c.bamfile
+
+
 proc main() =
   let args = docopt(doc, version="ALLHIC 0.7.11")
 
   if args["partition"]:
-    echo "Hello world"
+    partition_main()
 
   if args["optimize"]:
     optimize_main()

hic/partition.nim

@@ -0,0 +1,24 @@
+#
+# ALLHIC: Partition function
+# Given a target k, number of partitions, the goal of the partitioning is to
+# separate all the contigs into separate clusters. As with all clustering
+# algorithm, there is an optimization goal here.
+#
+# The LACHESIS algorithm is a hierarchical clustering algorithm using average
+# links.
+#
+
+
+import logging
+
+var logger = newConsoleLogger()
+logger.addHandler()
+
+type
+  Partitioner* = ref object
+    bamfile*: string
+
+
+proc initPartitioner*(bamfile: string): Partitioner =
+  new result
+  result.bamfile = bamfile

install.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+echo $(pwd)
+
+sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
+     curl  libssl-dev libtool autoconf automake libcurl4-openssl-dev
+
+export base=$(pwd)
+if [ ! -x nim-$BRANCH/bin/nim ]; then
+  git clone -b $BRANCH --depth 1 git://github.com/nim-lang/nim nim-$BRANCH/
+  cd nim-$BRANCH
+  git clone --depth 1 git://github.com/nim-lang/csources csources/
+  cd csources
+  sh build.sh
+  cd ..
+  rm -rf csources
+  bin/nim c koch
+  ./koch boot -d:release
+else
+  cd nim-$BRANCH
+  git fetch origin
+  if ! git merge FETCH_HEAD | grep "Already up-to-date"; then
+    bin/nim c koch
+    ./koch boot -d:release
+  fi
+fi
+
+export PATH=$PATH:$base/nim-$BRANCH/bin/:$PATH:$base/nimble/src
+cd $base
+echo $PATH
+
+
+git clone --depth 1 https://github.com/nim-lang/nimble.git
+cd nimble
+nim c src/nimble
+src/nimble install -y
+
+set -x
+cd $base
+nimble refresh
+
+echo $(which nimble)
+echo $(pwd)
+
+
+if [ ! -x hts-nim ]; then
+    cd $base
+    git clone --depth 1 https://github.com/brentp/hts-nim/
+    cd hts-nim && nimble install -y
+fi
+
+set -x
+cd $base
+nimble install -y
+git clone --recursive https://github.com/samtools/htslib.git
+
+cd htslib && git checkout 1.5 && autoheader && autoconf && ./configure --enable-libcurl
+cd ..
+make -j 4 -C htslib
+export LD_LIBRARY_PATH=$base/htslib
+ls -lh $base/htslib/*.so
+echo $base