added plink support, bumped version nr

Author: stschiff

Changelog.md

@@ -17,4 +17,6 @@ V 1.4.0.3: Updated to new sequence-formats version, now including reading of gen
 V 1.4.0.4:
 * Fixed eigenstrat-output in pileupCaller to add a dot after the outputprefix before the file extensions.
 * Updated haskell-stack wrapper scripts for EIGENSOFT and ADMIXTOOLS.
-* Moved unmaintained scripts into unmaintained folder.
+* Moved unmaintained scripts into unmaintained folder.
+
+V 1.5.0: Added support for Plink output

sequenceTools.cabal

@@ -1,5 +1,5 @@
 name:                sequenceTools
-version:             1.4.0.5
+version:             1.5.0
 synopsis:            A package with tools for processing DNA sequencing data
 description:         The tools in this package process sequencing Data, in particular from ancient DNA sequencing libraries. Key tool in this package is pileupCaller, a tool to randomly sample genotypes from sequencing data.
 license:             GPL-3

src-executables/pileupCaller.hs

@@ -206,16 +206,16 @@ initialiseEnvironment args = do
 runMain :: App ()
 runMain = do
     env_ <- ask
-    liftIO $ print env_
-    -- let pileupProducer = readPileupFromStdIn
-    -- snpFile <- asks envSnpFile
-    -- freqSumProducer <- pileupToFreqSum snpFile pileupProducer
-    -- outFormat <- asks envOutFormat
-    -- case outFormat of
-    --     FreqSumFormat -> outputFreqSum freqSumProducer
-    --     EigenstratFormat outPrefix popName -> outputEigenStratOrPlink outPrefix popName False freqSumProducer
-    --     PlinkFormat outPrefix popName -> outputEigenStratOrPlink outPrefix popName True freqSumProducer
-    -- outputStats
+    -- liftIO $ print env_
+    let pileupProducer = readPileupFromStdIn
+    snpFile <- asks envSnpFile
+    freqSumProducer <- pileupToFreqSum snpFile pileupProducer
+    outFormat <- asks envOutFormat
+    case outFormat of
+        FreqSumFormat -> outputFreqSum freqSumProducer
+        EigenstratFormat outPrefix popName -> outputEigenStratOrPlink outPrefix popName False freqSumProducer
+        PlinkFormat outPrefix popName -> outputEigenStratOrPlink outPrefix popName True freqSumProducer
+    outputStats
 
 pileupToFreqSum :: FilePath -> Producer PileupRow (SafeT IO) () ->
     App (Producer FreqSumEntry (SafeT IO) ())