samtools 0.2.4.1 → 0.2.4.2

raw patch · 6 files changed

+14/−3 lines, 6 files

Files

cbits/samtools.c +1/−0
include/samtools.h +1/−0
samtools-0.1.18/bam.h +2/−0
samtools.cabal +1/−1
src/Bio/SamTools/Bam.hs +5/−1
src/Bio/SamTools/LowLevel.chs +4/−1

cbits/samtools.c view

@@ -16,6 +16,7 @@ uint32_t bam_fsecondary(void) { return BAM_FSECONDARY; } uint32_t bam_fqcfail(void) { return BAM_FQCFAIL; } uint32_t bam_fdup(void) { return BAM_FDUP; }+uint32_t bam_fsupplementary(void) { return BAM_FSUPPLEMENTARY; }  uint32_t bam_cigar_mask(void) { return BAM_CIGAR_MASK; } uint32_t bam_cigar_shift(void) { return BAM_CIGAR_SHIFT; }

include/samtools.h view

@@ -17,6 +17,7 @@ uint32_t bam_fsecondary(void); uint32_t bam_fqcfail(void); uint32_t bam_fdup(void);+uint32_t bam_fsupplementary(void);  uint32_t bam_cigar_mask(void); uint32_t bam_cigar_shift(void);

samtools-0.1.18/bam.h view

@@ -115,6 +115,8 @@ #define BAM_FQCFAIL      512 /*! @abstract optical or PCR duplicate */ #define BAM_FDUP        1024+/*! @abstract this is a supplementary read */+#define BAM_FSUPPLEMENTARY 2048  #define BAM_OFDEC          0 #define BAM_OFHEX          1

samtools.cabal view

@@ -1,5 +1,5 @@ Name:                samtools-Version:             0.2.4.1+Version:             0.2.4.2 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-

src/Bio/SamTools/Bam.hs view

@@ -25,7 +25,7 @@   , Bam1, header   , targetID, targetName, targetLen, position   , isPaired, isProperPair, isUnmap, isMateUnmap, isReverse, isMateReverse-  , isRead1, isRead2, isSecondary, isQCFail, isDup+  , isRead1, isRead2, isSecondary, isQCFail, isDup, isSupplementary   , cigars, queryName, queryLength, querySeq, queryQual   , mateTargetID, mateTargetName, mateTargetLen, matePosition, insertSize     @@ -142,6 +142,10 @@ -- | Is the read a technical duplicate isDup :: Bam1 -> Bool isDup = isFlagSet flagDup++-- | Is the read a supplementary read+isSupplementary :: Bam1 -> Bool+isSupplementary = isFlagSet flagSupplementary  -- | CIGAR description of the alignment cigars :: Bam1 -> [Cigar]

src/Bio/SamTools/LowLevel.chs view

@@ -21,7 +21,7 @@                              , cigarOp, cigarLength                              , BamFlag(..)                              , flagPaired, flagProperPair, flagUnmap, flagMUnmap, flagReverse, flagMReverse-                             , flagRead1, flagRead2, flagSecondary, flagQCFail, flagDup+                             , flagRead1, flagRead2, flagSecondary, flagQCFail, flagDup, flagSupplementary                              , Bam1Ptr, Bam1Int                              , getTID, getPos, getFlag, getNCigar, getLQSeq, getMTID, getMPos, getISize                              , bam1Strand, bam1MStrand, bam1Cigar, bam1QName, bam1Seq, bam1Qual, bam1Seqi@@ -133,6 +133,9 @@  flagDup :: BamFlag flagDup = BamFlag {#call pure unsafe bam_fdup#}++flagSupplementary :: BamFlag+flagSupplementary = BamFlag {#call pure unsafe bam_fsupplementary#}  newtype BamCigar = BamCigar { unBamCigar :: CUInt }                    deriving (Eq, Show, Ord)