seqloc-datafiles 0.2.1.1 → 0.2.2

raw patch · 2 files changed

+8/−8 lines, 2 filesdep ~biocore

Dependency ranges changed: biocore

Files

• seqloc-datafiles.cabal +6/−6
• src/Bio/SeqLoc/Bed.hs +2/−2

@@ -1,5 +1,5 @@ Name:                seqloc-datafiles-Version:             0.2.1.1+Version:             0.2.2 Cabal-Version:       >= 1.4 Synopsis:            Read and write BED and GTF format genome annotations Description:         Read and write BED and GTF format genome annotations@@ -20,7 +20,7 @@   Other-modules:       Bio.SeqLoc.ZeptoUtils   Build-depends:       base >= 4.2 && < 5, bytestring,                        attoparsec >= 0.8.5, hashable, unordered-containers,-                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore+                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2   Hs-Source-Dirs:      src   Ghc-options:         -Wall @@ -29,7 +29,7 @@   Other-modules:       Bio.SeqLoc.GTF, Bio.SeqLoc.Bed, Bio.SeqLoc.ZeptoUtils   Build-depends:       base >= 4.2 && < 5, bytestring,                        attoparsec >= 0.8.5, hashable, unordered-containers,-                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore, transformers, monads-tf+                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2, transformers, monads-tf    Hs-Source-Dirs:      src   Ghc-options:         -Wall -rtsopts   C-Sources:           src/rtsopts.c@@ -41,7 +41,7 @@   Other-modules:       Bio.SeqLoc.GTF, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils   Build-depends:       base >= 4.2 && < 5, bytestring,                        attoparsec >= 0.8.5, hashable, unordered-containers,-                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore,+                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2,                        QuickCheck, random   Hs-Source-Dirs:      src, test   Ghc-options:         -Wall -rtsopts@@ -54,7 +54,7 @@   Other-modules:       Bio.SeqLoc.Bed, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils   Build-depends:       base >= 4.2 && < 5, bytestring,                        attoparsec >= 0.8.5, hashable, unordered-containers,-                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore,+                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2,                        QuickCheck, random   Hs-Source-Dirs:      src, test   Ghc-options:         -Wall@@ -66,7 +66,7 @@   Other-modules:       Bio.SeqLoc.GTF, Bio.SeqLoc.TranscriptTable, Bio.SeqLoc.ZeptoUtils   Build-depends:       base >= 4.2 && < 5, bytestring,                        attoparsec >= 0.8.5, hashable, unordered-containers,-                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore,+                       iteratee >= 0.8.1, seqloc >= 0.3.1, biocore >= 0.2,                        QuickCheck, random   Hs-Source-Dirs:      src, test   Ghc-options:         -Wall -rtsopts

@@ -126,8 +126,8 @@              fail $ "Bio.SeqLoc.Bed: bad sploc:" ++               (BS.unpack . BS.unwords $ [ repr loc, repr chromStart, repr chromEnd ])            cdsloc <- case liftM2 (,) thickStart thickEnd of-             Just (start, end) -> liftM Just $! bedCdsLoc loc start end-             Nothing -> return Nothing+             Just (start, end) | end > start -> liftM Just $! bedCdsLoc loc start end+             _ -> return Nothing            let n = toSeqLabel $ BS.copy name                c = toSeqLabel $ BS.copy chrom            return $! Transcript n n (OnSeq c loc) cdsloc