samtools 0.1.1 → 0.1.2

raw patch · 3 files changed

+19/−6 lines, 3 filesdep ~base

Dependency ranges changed: base

Files

• samtools.cabal +4/−4
• src/Bio/SamTools/Bam.hs +14/−1
• src/Bio/SamTools/Cigar.hs +1/−1

@@ -1,5 +1,5 @@ Name:                samtools-Version:             0.1.1+Version:             0.1.2 Synopsis:            Binding to the C samtools library Description:         Binding to the C samtools library, which reads and                      writes SAM format alignments, both binary and tab-@@ -10,7 +10,7 @@ License-file:        LICENSE Author:              Nicholas Ingolia Maintainer:          nick@ingolia.org-Category:            Bio+Category:            Bioinformatics Homepage:            http://www.ingolia-lab.org/software/samtools/  Build-type:          Simple@@ -33,7 +33,7 @@   Exposed-modules:     Bio.SamTools.Bam, Bio.SamTools.Cigar,                        Bio.SamTools.BamIndex, Bio.SamTools.FaIdx   Other-modules:       Bio.SamTools.LowLevel, Bio.SamTools.Internal, C2HS-  Build-depends:       base >= 4.3 && < 5, bytestring, haskell98, vector >= 0.7, seqloc+  Build-depends:       base >= 4.2 && < 5, bytestring, haskell98, vector >= 0.7, seqloc   Hs-Source-Dirs:      src   Build-tools:         c2hs   Include-dirs:        samtools-0.1.13, include@@ -63,7 +63,7 @@   Other-modules:       Bio.SamTools.Bam, Bio.SamTools.Cigar,                        Bio.SamTools.BamIndex, Bio.SamTools.FaIdx,                        Bio.SamTools.LowLevel, Bio.SamTools.Internal, C2HS-  Build-depends:       base >= 4.3 && < 5, bytestring, haskell98, vector >= 0.7, seqloc, process, filepath+  Build-depends:       base >= 4.2 && < 5, bytestring, haskell98, vector >= 0.7, seqloc, process, filepath   Hs-Source-Dirs:      src, test   Build-tools:         c2hs   Include-dirs:        samtools-0.1.13, include

@@ -26,7 +26,7 @@   , targetID, targetName, targetLen, position   , isPaired, isProperPair, isUnmap, isMateUnmap, isReverse, isMateReverse   , isRead1, isRead2, isSecondary, isQCFail, isDup-  , cigars, queryName, queryLength, querySeq+  , cigars, queryName, queryLength, querySeq, queryQual   , mateTargetID, mateTargetName, mateTargetLen, matePosition, insertSize        , nMismatch, nHits, matchDesc                                                               @@ -52,6 +52,7 @@ import Control.Exception import Control.Monad import Data.Bits+import qualified Data.ByteString as BSW import qualified Data.ByteString.Char8 as BS import Foreign hiding (new) import Foreign.C.Types@@ -164,6 +165,18 @@                 | otherwise = return $! Just $!                                BS.pack [ seqiToChar . bam1Seqi seqarr $ i | i <- [0..((fromIntegral l)-1)] ]   in getLQSeq p >>= getQSeq+     +-- | 'Just' the query qualities, or 'Nothing' when it is+-- unavailable. These are returned in ASCII format, i.e., /q/ + 33.+queryQual :: Bam1 -> Maybe BS.ByteString+queryQual b = unsafePerformIO $ withForeignPtr (ptrBam1 b) $ \p ->+  let getQQual l | l < 1 = return Nothing+                 | otherwise = do q0 <- peek $! bam1Qual p+                                  if q0 == 0xff+                                     then return Nothing+                                     else liftM (Just . BSW.map (+ 33)) $!+                                            BS.packCStringLen (castPtr $! bam1Qual p, fromIntegral l)+  in getLQSeq p >>= getQQual       seqiToChar :: CUChar -> Char seqiToChar = (chars V.!) . fromIntegral

@@ -75,7 +75,7 @@         entry start (Cigar SoftClip _len) = (start,       Nothing)         entry start (Cigar HardClip _len) = (start,       Nothing)         entry start (Cigar Pad      _len) = (start,       Nothing)-        contig start len = Just $! Loc.fromStartEnd (fromIntegral start) (fromIntegral $ start + len - 1)+        contig start len = Just $! Loc.fromBoundsStrand (fromIntegral start) (fromIntegral $ start + len - 1) Fwd  mergeAdj :: Loc.ContigLoc -> [Loc.ContigLoc] -> [Loc.ContigLoc] mergeAdj cprev [] = [cprev]