From d6e89da0b1466623a945146a5512108112131c4e Mon Sep 17 00:00:00 2001
From: Glenn Hickey <hickey@soe.ucsc.edu>
Date: Fri, 1 Nov 2013 09:00:37 -0700
Subject: [PATCH] add --prec option to halPhlyoP to control number of digits to
 write in wigs.  default remains 3

---
 phyloP/halPhyloPMP.py         | 6 +++++-
 phyloP/halTreePhyloP.py       | 6 ++++++
 phyloP/impl/halPhyloP.cpp     | 4 ----
 phyloP/impl/halPhyloPMain.cpp | 7 +++++++
 4 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/phyloP/halPhyloPMP.py b/phyloP/halPhyloPMP.py
index 1c63d0ed..18ce6daa 100755
--- a/phyloP/halPhyloPMP.py
+++ b/phyloP/halPhyloPMP.py
@@ -53,7 +53,8 @@ def getHalPhyloPCmd(options):
              opt == 'dupMask' or
              opt == 'step' or
              opt == 'refBed' or
-             opt == 'subtree')):
+             opt == 'subtree' or
+             opt == 'prec')):
             if val is not True:
                 cmd += ' --%s %s' % (opt, str(val))
             else:
@@ -270,6 +271,9 @@ def main(argv=None):
     hppGrp.add_argument("--subtree",
                         help="Subtree root for lineage-specific acceleration/conservation",
                         default=None)
+    hppGrp.add_argument("--prec",
+                        help="Number of decimal places in wig output", type=int,
+                        default=None)
 
     args = parser.parse_args()
 
diff --git a/phyloP/halTreePhyloP.py b/phyloP/halTreePhyloP.py
index 5adc1812..c4dd7758 100644
--- a/phyloP/halTreePhyloP.py
+++ b/phyloP/halTreePhyloP.py
@@ -58,6 +58,8 @@ def computeTreePhyloP(args):
             args.hal, genome, args.mod, bedFlags, args.numProc, wigFile)
         if args.subtree is not None:
             cmd += " --subtree %s" % args.subtree
+        if args.prec is not None:
+            cmd += " --prec %d" % args.prec
 
         runShellCommand(cmd)
     
@@ -117,6 +119,10 @@ def main(argv=None):
     parser.add_argument("--subtree",
                         help="Run clade-specific acceleration/conservation on subtree below this node",
                         default=None)
+    parser.add_argument("--prec",
+                        help="Number of decimal places in wig output", type=int,
+                        default=None)
+
     # need phyloP options here:
     
     args = parser.parse_args()
diff --git a/phyloP/impl/halPhyloP.cpp b/phyloP/impl/halPhyloP.cpp
index 546dd9f7..f4bf728b 100644
--- a/phyloP/impl/halPhyloP.cpp
+++ b/phyloP/impl/halPhyloP.cpp
@@ -54,10 +54,6 @@ void PhyloP::init(AlignmentConstPtr alignment, const string& modFilePath,
   _softMaskDups = (int)softMaskDups;
   _outStream = outStream;
 
-  // set float precision to 3 places to be consistent with non-hal phyloP
-  _outStream->setf(ios::fixed, ios::floatfield);
-  _outStream->precision(3);
-
   if (dupType == "ambiguous")
   {
     _maskAllDups = 0;
diff --git a/phyloP/impl/halPhyloPMain.cpp b/phyloP/impl/halPhyloPMain.cpp
index a9078179..5765de67 100644
--- a/phyloP/impl/halPhyloPMain.cpp
+++ b/phyloP/impl/halPhyloPMain.cpp
@@ -70,6 +70,7 @@ static CLParserPtr initParser()
 			   "leading up to this node), and test for "
 			   "conservation/acceleration in this subtree "
 			   "relative to the rest of the tree", "\"\"");
+  optionsParser->addOption("prec", "Number of decimal places in wig output", 3);
   
   optionsParser->setDescription("Make PhyloP wiggle plot for a genome.");
   return optionsParser;
@@ -90,6 +91,7 @@ int main(int argc, char** argv)
   hal_size_t length;
   hal_size_t step;
   string refBedPath;
+  hal_size_t prec;
   try
   {
     optionsParser->parseOptions(argc, argv);
@@ -106,6 +108,7 @@ int main(int argc, char** argv)
     subtree = optionsParser->getOption<string>("subtree");
     std::transform(dupMask.begin(), dupMask.end(), dupMask.begin(), ::tolower);
     refBedPath = optionsParser->getOption<string>("refBed");
+    prec = optionsParser->getOption<hal_size_t>("prec");
   }
   catch(exception& e)
   {
@@ -169,6 +172,10 @@ int main(int argc, char** argv)
       }
     }
     
+    // set the precision of floating point output
+    outStream.setf(ios::fixed, ios::floatfield);
+    outStream.precision(prec);
+    
     PhyloP phyloP;
     phyloP.init(alignment, modPath, &outStream, dupMask == "soft" , dupType,
 		"CONACC", subtree);