sequence-formats 1.5.1.3 → 1.5.1.4

raw patch · 3 files changed

+13/−2 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• Changelog.md +2/−0
• sequence-formats.cabal +1/−1
• src/SequenceFormats/Plink.hs +10/−1

@@ -1,3 +1,5 @@+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).+ V 1.5.1.3: added possibility to parse allele names 01234 in bim files.  V 1.5.1.2: added readPlink to export list of Plink module.

@@ -1,5 +1,5 @@ name:                sequence-formats-version:             1.5.1.3+version:             1.5.1.4 synopsis:            A package with basic parsing utilities for several Bioinformatic data formats. description:         Contains utilities to parse and write Eigenstrat, Fasta, FreqSum, VCF, Plink and other file formats used in population genetics analyses. license:             GPL-3

@@ -39,7 +39,16 @@     ref        <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGN01234")     alt        <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGX01234")     void A.endOfLine-    return $ EigenstratSnpEntry (Chrom chrom) pos geneticPos snpId_ ref alt+    let refConvert = convertNum ref+        altConvert = convertNum alt+    return $ EigenstratSnpEntry (Chrom chrom) pos geneticPos snpId_ refConvert altConvert+  where+    convertNum '0' = 'N'+    convertNum '1' = 'A'+    convertNum '2' = 'C'+    convertNum '3' = 'G'+    convertNum '4' = 'T'+    convertNum x   = x  famParser :: A.Parser EigenstratIndEntry famParser = do