adding minimap2 map-ont support

.gitmodules

@@ -37,3 +37,6 @@
 [submodule "submodules/cPecan"]
 	path = submodules/cPecan
 	url = https://github.com/benedictpaten/cPecan.git
+[submodule "submodules/minimap2"]
+	path = submodules/minimap2
+	url = https://github.com/lh3/minimap2

src/executionScript.sh

@@ -18,7 +18,7 @@ fi
 export PYTHONPATH=${BASEDIR}/src:${BASEDIR}/submodules
 
 #Set the path to just the relevant directories
-export PATH=${BASEDIR}/submodules/sonLib/bin:${BASEDIR}/submodules/jobTree/bin:${BASEDIR}/submodules/bwa/:${BASEDIR}/submodules/last/src/:${BASEDIR}/submodules/last/scripts/:${PATH}
+export PATH=${BASEDIR}/submodules/sonLib/bin:${BASEDIR}/submodules/jobTree/bin:${BASEDIR}/submodules/bwa/:${BASEDIR}/submodules/last/src/:${BASEDIR}/submodules/last/scripts/:${BASEDIR}/submodules/minimap2/:${PATH}
 
 #Run described script
 python $@

src/margin/mappers/minimap2.py

@@ -0,0 +1,20 @@
+from margin.mappers.abstractMapper import AbstractMapper
+from sonLib.bioio import system
+import os
+
+class Minimap2(AbstractMapper):
+    def run(self, args="-ax map-ont"):
+        localReferenceFastaFile = os.path.join(self.getLocalTempDir(), "ref.fa") #Because BWA builds these crufty index files, copy to a temporary directory
+        system("cp %s %s" % (self.referenceFastaFile, localReferenceFastaFile))
+        system("minimap2 %s %s %s > %s" % (args, localReferenceFastaFile, self.readFastqFile, self.outputSamFile))
+
+class Minimap2Chain(Minimap2):
+    def run(self):
+        Minimap2.run(self)
+        self.chainSamFile()
+
+class Minimap2Realign(Minimap2):
+    def run(self):
+        Minimap2.run(self)
+        self.realignSamFile()
+

src/margin/marginAlign.py

@@ -6,6 +6,7 @@
 from jobTree.scriptTree.stack import Stack
 from margin.mappers.last import Last, LastChain, LastRealign
 from margin.mappers.bwa import Bwa, BwaChain, BwaRealign
+from margin.mappers.minimap2 import Minimap2, Minimap2Chain, Minimap2Realign
 from margin.utils import pathToBaseNanoporeDir
 import cPecan.cPecanEm
 from cPecan.cPecanEm import addExpectationMaximisationOptions
@@ -30,6 +31,8 @@ def main():
                       default=0.5, type=float)
     parser.add_option("--matchGamma", dest="matchGamma", help="Set the match gamma for the AMAP function", 
                       default=0.0, type=float)
+    parser.add_option("--minimap2", dest="minimap2", help="Use minimap2 (map-ont) instead of LAST", 
+                      default=False, action="store_true")
 
     #Add the cPecan expectation maximisation options
     options = cPecan.cPecanEm.Options()
@@ -71,11 +74,26 @@ def main():
     #Set the mapper
     if options.noRealign:
         if options.noChain: # i.e. --noChain --noRealign
-            mapper = Bwa if options.bwa else Last
+            if options.bwa:
+                mapper = Bwa
+            elif options.minimap2:
+                mapper = Minimap2
+            else:
+                mapper = Last
         else: # i.e. --noRealign
-            mapper = BwaChain if options.bwa else LastChain
+            if options.bwa:
+                mapper = BwaChain
+            elif options.minimap2:
+                mapper = Minimap2Chain
+            else:
+                mapper = LastChain
     else:
-        mapper = BwaRealign if options.bwa else LastRealign
+        if options.bwa:
+	    mapper = BwaRealign
+        elif options.minimap2:
+	    mapper = Minimap2Realign
+        else:
+	    mapper = LastRealign
 
     #This line invokes jobTree  
     i = Stack(mapper(readFastqFile=args[0], referenceFastaFile=args[1], outputSamFile=args[2], 

submodules/Makefile

@@ -1,5 +1,5 @@
 # order is important, libraries first
-modules = sonLib jobTree bwa last cPecan
+modules = sonLib jobTree bwa last cPecan minimap2
 .PHONY: all %.all clean %.clean
 
 all : ${modules:%=all.%} 

tests/tests.py

@@ -132,6 +132,12 @@ def testMarginAlignBwa(self):
     def testMarginAlignBwaNoRealign(self):
         self.runMarginAlign(self.readFastqFile1, self.referenceFastaFile1, "--bwa --noRealign")
 
+    def testMarginAlignMinimap2(self):
+        self.runMarginAlign(self.readFastqFile1, self.referenceFastaFile1, "--minimap2")
+
+    def testMarginAlignMinimap2NoRealign(self):
+        self.runMarginAlign(self.readFastqFile1, self.referenceFastaFile1, "--minimap2 --noRealign")
+
     #The following tests marginCaller
 
     def runMarginCaller(self, samFile, referenceFastaFile, mutationsFile, args=""):