fixed a few bugs

exampleData/fourPop.histogram.txt

@@ -1,8 +1,7 @@
 NAMES=EUR,SEA,SIB,FAM
 N=66,44,44,28
 MAX_M=10
-0,0,0,0 2159959569
-HIGHER 3462654
+TOTAL_SITES=2170616682
 1,0,0,0 1525898
 0,1,0,0 1075097
 0,0,1,0 818979

src-rarecoal/Main.hs

@@ -185,11 +185,11 @@ parseHistOpts = HistogramOptions <$> parseHistPath <*> parseMinAf <*>
         \square-brackets. Gives all branches (as 0-based indices) in which you \
         \require at least one derived allele for the computation of the \
         \likelihood. This is useful for mapping ancient samples onto a tree" <>
-        OP.value [] <> OP.hidden
+        OP.value [] <> OP.showDefault
     parseExcludePattern = OP.option OP.auto $ OP.long "excludePattern" <>
         OP.metavar "[INT,INT,...]" <> OP.help "a comma-separated list without \
         \spaces and surrounded by square-brackets. Gives a pattern to exclude \
-        \from fitting. Can be given multiple times" <> OP.hidden
+        \from fitting. Can be given multiple times" <> OP.hidden <> OP.value [] <> OP.showDefault
 
 parseMaxl :: OP.Parser Command
 parseMaxl = CmdMaxl <$> parseMaxlOpt

src-rarecoal/Maxl.hs

@@ -2,7 +2,7 @@
 module Maxl (runMaxl, MaxlOpt(..)) where
 
 import Rarecoal.ModelTemplate (ModelTemplate(..), instantiateModel, getModelTemplate, 
-    ModelOptions(..), ParamOptions(..), makeParameterDict, getParamNames)
+    ModelOptions(..), ParamOptions(..), makeParameterDict, getParamNames, fillParameterDictWithDefaults)
 import Rarecoal.Utils (GeneralOptions(..), HistogramOptions(..), setNrProcessors, loadHistogram)
 import Rarecoal.MaxUtils (penalty, minFunc, computeFrequencySpectrum, 
     writeFullFitTable, writeSummaryFitTable, makeInitialPoint)
@@ -30,7 +30,8 @@ runMaxl :: MaxlOpt -> Script ()
 runMaxl opts = do
     scriptIO $ setNrProcessors (maGeneralOpts opts)
     modelTemplate <- getModelTemplate (maModelOpts opts)
-    modelParams <- scriptIO $ makeParameterDict (maParamOpts opts)
+    modelParams <- (scriptIO $ makeParameterDict (maParamOpts opts)) >>= 
+        fillParameterDictWithDefaults modelTemplate
     _ <- tryRight $ instantiateModel (maGeneralOpts opts) modelTemplate modelParams
     let modelBranchNames = mtBranchNames modelTemplate
     hist <- loadHistogram (maHistogramOpts opts) modelBranchNames

src-rarecoal/Mcmc.hs

@@ -2,7 +2,7 @@ module Mcmc (runMcmc, McmcOpt(..)) where
 
 import Rarecoal.Utils (GeneralOptions(..), HistogramOptions(..), setNrProcessors)
 import Rarecoal.ModelTemplate (ModelTemplate(..), ParamOptions(..), ModelOptions(..), 
-    getModelTemplate, instantiateModel, getParamNames, makeParameterDict)
+    getModelTemplate, instantiateModel, getParamNames, makeParameterDict, fillParameterDictWithDefaults)
 import Rarecoal.Utils (loadHistogram)
 import Rarecoal.MaxUtils (minFunc, penalty, writeFullFitTable, writeSummaryFitTable, 
     makeInitialPoint, computeFrequencySpectrum)
@@ -49,7 +49,8 @@ runMcmc :: McmcOpt -> Script ()
 runMcmc opts = do
     scriptIO $ setNrProcessors (mcGeneralOpts opts)
     modelTemplate <- getModelTemplate (mcModelOpts opts)
-    modelParams <- scriptIO $ makeParameterDict (mcParamOpts opts)
+    modelParams <- (scriptIO $ makeParameterDict (mcParamOpts opts)) >>= 
+        fillParameterDictWithDefaults modelTemplate
     _ <- tryRight $ instantiateModel (mcGeneralOpts opts) modelTemplate modelParams
     let modelBranchNames = mtBranchNames modelTemplate
     hist <- loadHistogram (mcHistogramOpts opts) modelBranchNames

src/Rarecoal/ModelTemplate.hs

@@ -19,7 +19,6 @@ import           Control.Monad.Trans.Except           (throwE)
 import           Data.Char                            (isAlphaNum)
 -- import Debug.Trace (trace)
 import           Data.List                            (elemIndex, nub)
-import           Data.Maybe                           (catMaybes)
 import qualified Data.Text                            as T
 import qualified Data.Text.IO                         as T
 import qualified Text.Parsec                          as P
@@ -72,7 +71,8 @@ getModelTemplate mo = do
             ", constraints "%w%" and parameters "%w) n e c paramNames
 
 modelTemplateP :: Parser ModelTemplate
-modelTemplateP = ModelTemplate <$> parseBranchNames <*> parseEvents <*> parseConstraints
+modelTemplateP = ModelTemplate <$> parseBranchNames <*> parseEvents <*>
+    (parseConstraints <|> pure [])
 
 parseBranchNames :: Parser [T.Text]
 parseBranchNames = PC.string "BRANCHES" *> PC.spaces *> PC.char '=' *> PC.spaces *> PC.char '[' *> 
@@ -259,17 +259,17 @@ fillParameterDictWithDefaults :: ModelTemplate -> [(T.Text, Double)] ->
     Script [(T.Text, Double)]
 fillParameterDictWithDefaults mt paramsDict = do
     let paramNames = getParamNames mt
-    fmap catMaybes . forM paramNames $ \p ->
+    forM paramNames $ \p ->
         case p `lookup` paramsDict of
-            Just _ -> return Nothing
+            Just v -> return (p, v)
             Nothing | T.head p == 'p' -> do
                         scriptIO . errLn $
                             format ("setting parameter "%w%" = 1.0 (default)") p
-                        return $ Just (p, 1.0)
+                        return (p, 1.0)
                     | T.take 3 p == "adm" -> do
                         scriptIO . errLn $ format ("setting parameter "%w%
-                            " = 0.05 (d efault)") p
-                        return $ Just (p, 0.05)
+                            " = 0.05 (default)") p
+                        return (p, 0.05)
                     | otherwise ->
                         throwE $ format ("Don't know how to initialize \
                         \parameter "%w%". Please provide initial \

src/Rarecoal/ModelTemplate/Test.hs

@@ -1,7 +1,6 @@
 {-# LANGUAGE OverloadedStrings #-}
 module Rarecoal.ModelTemplate.Test (tests) where
 
-import Rarecoal.Utils (defaultTimes)
 import Rarecoal.ModelTemplate (ModelTemplate(..), MTEvent(..), MTConstraint(..), ParamSpec(..),
     ConstraintOperator(..), getModelTemplate, ModelOptions(..))