sequence-formats 1.6.1 → 1.6.3

raw patch · 8 files changed

+11/−8 lines, 8 filesdep ~base

Dependency ranges changed: base

Files

• Changelog.md +3/−0
• sequence-formats.cabal +1/−1
• src/SequenceFormats/FreqSum.hs +2/−2
• src/SequenceFormats/Pileup.hs +1/−1
• src/SequenceFormats/Plink.hs +1/−1
• src/SequenceFormats/RareAlleleHistogram.hs +1/−1
• src/SequenceFormats/Utils.hs +1/−1
• testDat/example.pileup +1/−1

@@ -1,3 +1,6 @@+V 1.6.3: Pileup reference-base is read as upper case, even if it's not in the file.+V 1.6.2: Made compatible with GHC 9 (thanks to github user sjakobi)+ V 1.6.0: Plink Output now supported.  V 1.5.1.4: Plink BIM parsing now automatically converts from Numbers (0,1,2,3,4) to Letters (N,A,C,T,G).

@@ -1,6 +1,6 @@ cabal-version:      >=1.10 name:               sequence-formats-version:            1.6.1+version:            1.6.3 license:            GPL-3 license-file:       LICENSE maintainer:         stephan.schiffels@mac.com

@@ -7,7 +7,7 @@ module SequenceFormats.FreqSum (readFreqSumStdIn, readFreqSumFile, FreqSumEntry(..),       FreqSumHeader(..), printFreqSumStdOut, printFreqSumFile, freqSumEntryToText) where -import SequenceFormats.Utils (consumeProducer, Chrom(..))+import SequenceFormats.Utils (consumeProducer, Chrom(..), readFileProd)  import Control.Applicative ((<|>)) import Control.Monad.Catch (MonadThrow, throwM)@@ -73,7 +73,7 @@  -- |A function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines. readFreqSumFile :: (MonadSafe m) => FilePath -> m (FreqSumHeader, Producer FreqSumEntry m ())-readFreqSumFile file = readFreqSumProd $ withFile file ReadMode PB.fromHandle+readFreqSumFile = readFreqSumProd . readFileProd  parseFreqSumHeader :: A.Parser FreqSumHeader parseFreqSumHeader = do

@@ -41,7 +41,7 @@     _ <- A.space     pos <- A.decimal     _ <- A.space-    refA <- A.satisfy (A.inClass "ACTGNactgnM")+    refA <- toUpper <$> A.satisfy (A.inClass "ACTGNactgnM")      -- for some reason, there is an M in the human reference at      -- position 3:60830534 (both in hs37d5 and in hg19)     _ <- A.space

@@ -100,7 +100,7 @@  -- |A function to read a bed file from a file. Returns a Producer over all lines. readPlinkBedFile :: (MonadSafe m) => FilePath -> Int -> m (Producer GenoLine m ())-readPlinkBedFile file nrInds = readPlinkBedProd nrInds (PS.withFile file ReadMode PB.fromHandle)+readPlinkBedFile file nrInds = readPlinkBedProd nrInds (readFileProd file)  -- |Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries. readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()

@@ -93,7 +93,7 @@ -- |Read a histogram from a File Handle. readHistogramFromHandle :: (MonadIO m) => Handle -> m RareAlleleHistogram readHistogramFromHandle handle = do-    res <- evalStateT (parse parseHistogram) . PB.fromHandle $ handle+    res <- evalStateT (parse parseHistogram) (PB.fromHandle handle)     case res of         Nothing -> throw (SeqFormatException "histogram file exhausted too early")         Just (Left err) -> throw (SeqFormatException ("Histogram parsing error: " <> show err))

@@ -73,7 +73,7 @@ consumeProducer parser prod = parsed parser prod >>= liftParsingErrors  readFileProd :: (PS.MonadSafe m) => FilePath -> Producer B.ByteString m ()-readFileProd f = PS.withFile f ReadMode PB.fromHandle+readFileProd f = PS.withFile f ReadMode (\h -> PB.fromHandle h)  word :: A.Parser B.ByteString word = A.takeTill isSpace

@@ -1,3 +1,3 @@ 1 1000 A 4 ..,C*. IIII 3 ..ac* III 8 ,,.,ccAA-3acccA IIIIIIII-1 2000 C 4 ..C+4IIIIa IIII 3 ACt..* III 8 .a.a.C.C* IIIIIIII+1 2000 c 4 ..C+4IIIIa IIII 3 ACt..* III 8 .a.a.C.C* IIIIIIII 2 1000 G 4 ,,.,,..-3AccC*. IIII 3 .,,* III 8 .,,.,,* IIIIIIII