updated cabal file, updated to pedantic compilation

of latest GHC

Author: stschiff

Changelog.md

@@ -1,5 +1,6 @@
 # Changelog
 
+- V 1.5.3.1: updated to latest GHC pedantic compilation
 - V 1.5.3: Upgraded to sequence-formats 1.7.0 introducing an option for plink popName encoding, and improved pileup-Parsing to allow for skip-reference characters
 - V 1.5.2: Fixed a bug with --samplePopName having to be entered after -p or -e. Fixed a bug in the sequence-formats dependency.
 - V 1.5.1: Added automatic building

sequenceTools.cabal

@@ -1,5 +1,5 @@
 name:                sequenceTools
-version:             1.5.3
+version:             1.5.3.1
 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
@@ -9,6 +9,8 @@ maintainer:          stephan.schiffels@mac.com
 category:            Bioinformatics
 build-type:          Simple
 cabal-version:       >=1.10
+Homepage:	         https://github.com/stschiff/sequenceTools
+Bug-Reports:         https://github.com/stschiff/sequenceTools/issues
 extra-source-files:  README.md,
                      Changelog.md
 

src-executables/pileupCaller.hs

@@ -323,9 +323,9 @@ outputEigenStratOrPlink outPrefix popName maybePlinkPopMode freqSumProducer = do
             RandomCalling -> True
             MajorityCalling _ -> True
             RandomDiploidCalling -> False
-    let [snpOut, indOut, genoOut] = case maybePlinkPopMode of
-            Just _  -> map (outPrefix <>) [".bim", ".fam", ".bed"]
-            Nothing -> map (outPrefix <>) [".snp", ".ind", ".geno"]
+    let (snpOut, indOut, genoOut) = case maybePlinkPopMode of
+            Just _  -> (outPrefix <> ".bim", outPrefix <> ".fam", outPrefix <> ".bed")
+            Nothing -> (outPrefix <> ".snp", outPrefix <> ".ind", outPrefix <> ".geno")
     let indEntries = [EigenstratIndEntry n Unknown popName | n <- sampleNames]
     let writeFunc = case maybePlinkPopMode of
             Nothing -> (\g s i -> writeEigenstrat g s i indEntries)

stack.yaml

@@ -1,4 +1,4 @@
-resolver: lts-18.28
+resolver: lts-20.17
 packages:
 - '.'
 extra-deps: