samtools 0.2.4.2 → 0.2.4.3

raw patch · 3 files changed

+7/−4 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• samtools.cabal +1/−1
• src/Bio/SamTools/Bam.hs +3/−3
• src/Bio/SamTools/LowLevel.chs +3/−0

@@ -1,5 +1,5 @@ Name:                samtools-Version:             0.2.4.2+Version:             0.2.4.3 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-

@@ -426,7 +426,7 @@ withBamInFile :: FilePath -> (InHandle -> IO a) -> IO a withBamInFile filename = bracket (openBamInFile filename) closeInHandle --- | Reads one alignment from an input handle, or returns @Nothing@ for end-of-file+-- | Read one alignment from an input handle, or returns @Nothing@ for end-of-file get1 :: InHandle -> IO (Maybe Bam1) get1 inh = withMVar (samfile inh) $ \fsam -> do   b <- bamInit1@@ -439,7 +439,7 @@     else do bptr <- newForeignPtr bamDestroy1Ptr b             return . Just $ Bam1 { ptrBam1 = bptr, header = inHeader inh } --- | Read a BAM file as a lazy strem of 'Bam1' records.+-- | Read a BAM file as a lazy stream of 'Bam1' records. readBams :: FilePath -> IO [Bam1] readBams = openBamInFile >=> getBams    where@@ -482,7 +482,7 @@ withBamOutFile :: FilePath -> Header -> (OutHandle -> IO a) -> IO a withBamOutFile filename hdr = bracket (openBamOutFile filename hdr) closeOutHandle --- | Writes one alignment to an input handle.+-- | Write one alignment to an output handle. --  -- There is no validation that the target sequence set of the output -- handle matches the target sequence set of the alignment.

@@ -58,6 +58,9 @@ #define __AVAILABILITY__ #define __OSX_AVAILABLE_STARTING(_mac, _iphone) #define __OSX_AVAILABLE_BUT_DEPRECATED(_macIntro, _macDep, _iphoneIntro, _iphoneDep) +#define __OSX_AVAILABLE_BUT_DEPRECATED_MSG(_macIntro, _macDep, _iphoneIntro, _iphoneDep, _warn_string) +#define __WATCHOS_PROHIBITED+#define __TVOS_PROHIBITED #endif  #include "faidx.h"