pv_      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh+Instance for special casing null pointers. ijk;Given a bit pattern, yield all bit masks that it contains. I This does *not* attempt to compute a minimal set of bit masks that when G combined yield the bit pattern, instead all contained bit masks are  produced. lIntegral conversion mFloating conversion nObtain C value from Haskell o. pObtain Haskell o from C value. q$Convert a C enumeration to Haskell. r$Convert a Haskell enumeration to C. Xstuvwxyz{|}~      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~_`abcdefghijklmnpqr_`abcdefghijklmnpqr      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^f  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\f  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\ 'Input handle for an indexed fasta file _Name of the fasta file `Open an indexed fasta file aBFetch a region specified by sequence name and coordinates, or the . empty string when the sequence is not found. Sequence name &(Starting, ending) position, 0-based b SAM/BAM format alignment cde *Target sequences from a SAM alignment set fg =Information about one target sequence in a SAM alignment set Target sequence name Target sequence lengh hNumber of target sequences %Returns the list of target sequences :Returns a target sequence by ID, which is a 0-based index %Returns a target sequence name by ID cde fg hcdecde fgfg  hCigar entry including length Cigar entry types Deletion from padded reference 'Trimmed nucleotides, removed from read +Trimmed nucleotides, still present in read &Skipped reference bases, i.e., splice )Deletion from read relative to reference (Insertion in read relative to reference /Aligned nucleotide, may be a match or mismatch ij  Convert a BAM binary cigar integer to a  !k" !" !" !"<#Handle for writing SAM/BAM format alignments lmn$'Target sequence set for the alignments %Handle for reading SAM/BAM format alignments opq&'Target sequence set for the alignments 'r8 the reference target sequence ID in the target set, or  s for an unmapped read (r the target sequence name, or s for an unmapped  read )r- the total length of the target sequence, or s for  an unmapped read *r; the 0-based index of the leftmost aligned position on the  target sequence, or s for an unmapped read t+Is the read paired ,RIs the pair properly aligned (usually based on relative orientation and distance) -Is the read unmapped .)Is the read paired and the mate unmapped /Is the fragment'+s reverse complement aligned to the target 0Is the read paired and the mate'+s reverse complement aligned to the target 14Is the fragment from the first read in the template 25Is the fragment from the second read in the template 3$Is the fragment alignment secondary 4#Did the read fail quality controls 5"Is the read a technical duplicate 6#CIGAR description of the alignment 7Name of the query sequence 8r& the length of the query sequence, or s when it is  unavailable. 9r the query sequence, or s when it is unavailable :r the query qualities, or s when it is 8 unavailable. These are returned in ASCII format, i.e., q + 33. u;r6 the target ID of the mate alignment target reference  sequence, or s* when the mate is unmapped or the read is  unpaired. <r; the name of the mate alignment target reference sequence,  or s4 when the mate is unmapped or the read is unpaired. =r3 the length of the mate alignment target reference  sequence, or s* when the mate is unmapped or the read is  unpaired. >'=Just the 0-based coordinate of the left-most position in the " mate alignment on the target, or s when the read is # unpaired or the mate is unmapped. ?r the total insert length, or s when the length is B unavailable, e.g. because the read is unpaired or the mated read B pair do not align in the proper relative orientation on the same  strand. @r* the match descriptor alignment field, or s when it  is absent Ar' the number of reported alignments, or s when this  information is not present. Br/ the number of mismatches in the alignemnt, or s & when this information is not present Cr0 the reference sequence location covered by the D alignment. This includes nucleotide positions that are reported to = be deleted in the read, but not skipped nucleotide position ? (typically intronic positions in a spliced alignment). If the E reference location is unavailable, e.g. for an unmapped read or for 9 a read with no CIGAR format alignment information, then s. Dr) the reference sequence location (as per C) on  the target reference (as per () vE1Open a TAM (tab-delimited text) format file with @SQ headers  for the target sequence set. FAOpen a TAM format file with a separate target sequence set index G Open a BAM (binary) format file wH Close a SAM/"BAM format alignment input handle ATarget sequence set data is still available after the file input  has been closed. IBRun an IO action using a handle to a TAM format file that will be  opened (see E) and closed for the action. JAs I0 with a separate target sequence index set (see  F) KAs I for BAM (binary) format files L5Reads one alignment from an input handle, or returns Nothing for end-of-file M#Read a BAM file as a lazy strem of  records. xNOpen a TAM format file with @SQ headers for writing alignments O.Open a BAM format file for writing alignments P!Close an alignment output handle QRS)Writes one alignment to an input handle. BThere is no validation that the target sequence set of the output : handle matches the target sequence set of the alignment. = #$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRS? '()*+,-./0123456789:;<=>?BA@CD%&&EFGHIJKLM#$$NOPQRS1#$$%&&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTyUzV@Handle for fetching alignments by region from a sorted, indexed  BAM file. {W%Filename of sorted, indexed BAM file |XTarget sequences Y/Open a sorted, indexed BAM file. Z}[\~]^ Use a BAM index file to extract  records aligned to a : specific target sequence (chromosome) number and region. TUVWXYZ[\]^VWXWXYZ[TUU\]^ TUUVWXWXYZ[\]^      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]  ^_`abcdefghijklmnopqrstuvwxyzrs{x|}x|~x|x|xyxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x x x x xxxxxxxxxxxxxxxxxxx x!x"x#x$x%x&x'x(x)x*x+x,x-x.x/x0x1x2x3x4x5x6x7x8x9x:x;x<x=>x=?x=@x=Ax=Bx=Cx=Dx=Ex=Fx=Gx=Hx=Ix=Jx=Kx=Lx=Mx=Nx=Ox=Px=QxRSxRTxRUxRVxRWxRXxRYxRZxR[xR\x]^x]_x]`x]ax]bx]cxdexdfxdgxdhxdixdjxdkxdlxdmxnoxpqxprxpsxptxpuxvwxvxxvyxvzxv{xv|xv}x~xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxyxyxyxyxxxxxxxxxxxxxxxxxxxxxxxxxxx      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~)xxY[samtools-0.2.1Bio.SamTools.FaIdxBio.SamTools.BamBio.SamTools.CigarBio.SamTools.BamIndexC2HSBio.SamTools.LowLevelBio.SamTools.InternalInHandlefilenameopenclosewithFastaIndexfetchfetchLocreadLocBam1Header HeaderSeqnamelennTargets targetSeqList targetSeq targetSeqName targetSeqLen lookupTargetCigarcigarlength CigarTypePadHardClipSoftClipRefSkipDelInsMatchtoCigar cigarToSpLoccigarToAlignment OutHandle outHeaderinHeadertargetID targetName targetLenpositionisPaired isProperPairisUnmap isMateUnmap isReverse isMateReverseisRead1isRead2 isSecondaryisQCFailisDupcigars queryName queryLengthquerySeq queryQual mateTargetIDmateTargetName mateTargetLen matePosition insertSize matchDescnHits nMismatchrefSpLoc refSeqLoc openTamInFileopenTamInFileWithIndex openBamInFile closeInHandle withTamInFilewithTamInFileWithIndex withBamInFileget1readBamsopenTamOutFileopenBamOutFilecloseOutHandlewithTamOutFilewithBamOutFileput1QueryqyHandle IdxHandle idxFilename idxHeader withIndexquerynext readBamRegion withIntConv withFloatConv peekIntConv peekFloatConvwithBoolpeekBoolwithEnumpeekEnum nothingIf nothingIfNullcombineBitMaskscontainsBitMaskextractBitMaskscIntConv cFloatConv cFromBoolghc-prim GHC.TypesBoolcToBoolcToEnum cFromEnumbase GHC.Stable newStablePtrIntGHC.IntInt8Int16Int32Int64 StablePtrGHC.WordWord8Word16Word32Word64GHC.PtrPtrFunPtrGHC.ForeignPtr ForeignPtrForeignunsafePerformIOForeign.MarshalunsafeLocalStateForeign.Marshal.PoolpooledNewArray0pooledNewArray pooledNewpooledReallocArray0pooledReallocArraypooledMallocArray0pooledMallocArraypooledReallocBytes pooledReallocpooledMallocBytes pooledMallocwithPoolfreePoolnewPoolPoolForeign.C.ErrorerrnoToIOErrorthrowErrnoPathIfMinus1_throwErrnoPathIfMinus1throwErrnoPathIfNullthrowErrnoPathIf_throwErrnoPathIfthrowErrnoPaththrowErrnoIfNullRetryMayBlockthrowErrnoIfNullRetrythrowErrnoIfNull throwErrnoIfMinus1RetryMayBlock_throwErrnoIfMinus1RetryMayBlockthrowErrnoIfMinus1Retry_throwErrnoIfMinus1RetrythrowErrnoIfMinus1_throwErrnoIfMinus1throwErrnoIfRetryMayBlock_throwErrnoIfRetry_throwErrnoIfRetryMayBlockthrowErrnoIfRetry throwErrnoIf_ throwErrnoIf throwErrno resetErrnogetErrno isValidErrnoeXDEV eWOULDBLOCKeUSERSeTXTBSY eTOOMANYREFS eTIMEDOUTeTIMEeSTALEeSRMNTeSRCHeSPIPEeSOCKTNOSUPPORT eSHUTDOWNeRREMOTE eRPCMISMATCHeROFSeREMOTEeREMCHGeRANGE ePROTOTYPEePROTONOSUPPORTePROTO ePROGUNAVAIL ePROGMISMATCH ePROCUNAVAILePROCLIMePIPE ePFNOSUPPORTePERM eOPNOTSUPPeNXIOeNOTTYeNOTSOCK eNOTEMPTYeNOTDIReNOTCONNeNOTBLKeNOSYSeNOSTReNOSReNOSPC eNOPROTOOPTeNONETeNOMSGeNOMEMeNOLINKeNOLCKeNOEXECeNOENTeNODEVeNODATAeNOBUFSeNFILE eNETUNREACH eNETRESETeNETDOWN eNAMETOOLONG eMULTIHOPeMSGSIZEeMLINKeMFILEeLOOPeISDIReISCONNeIOeINVALeINTR eINPROGRESSeILSEQeIDRM eHOSTUNREACH eHOSTDOWNeFTYPEeFBIGeFAULTeEXISTeDQUOTeDOMeDIRTY eDESTADDRREQeDEADLK eCONNRESET eCONNREFUSED eCONNABORTEDeCOMMeCHILDeBUSYeBADRPCeBADMSGeBADFeALREADYeAGAIN eAFNOSUPPORTeADV eADDRNOTAVAIL eADDRINUSEeACCESe2BIGeOKErrnoForeign.C.StringwithCWStringLen withCWStringnewCWStringLen newCWStringpeekCWStringLen peekCWStringwithCAStringLen withCAStringnewCAStringLen newCAStringpeekCAStringLen peekCAStringcastCharToCSCharcastCSCharToCharcastCharToCUCharcastCUCharToCharcastCharToCCharcastCCharToCharcharIsRepresentablewithCStringLen withCString newCStringLen newCStringpeekCStringLen peekCStringCString CStringLenCWString CWStringLenForeign.Marshal.Array advancePtr lengthArray0 moveArray copyArray withArrayLen0 withArray0 withArrayLen withArray newArray0newArray pokeArray0 pokeArray peekArray0 peekArray reallocArray0 reallocArray allocaArray0 allocaArray mallocArray0 mallocArrayForeign.Marshal.Utils moveBytes copyByteswithMany maybePeek maybeWithmaybeNewtoBoolfromBoolwithnewForeign.Marshal.Errorvoid throwIfNull throwIfNeg_ throwIfNegthrowIf_throwIfForeign.Marshal.Allocfree reallocBytesreallocallocaBytesAligned allocaBytesalloca mallocBytesmalloc finalizerFreeForeign.ForeignPtrunsafeForeignPtrToPtrForeign.ForeignPtr.ImpmallocForeignPtrArray0mallocForeignPtrArraynewForeignPtrEnvwithForeignPtr newForeignPtr Foreign.Ptr intPtrToPtr ptrToIntPtr wordPtrToPtr ptrToWordPtrfreeHaskellFunPtrWordPtrIntPtrfinalizeForeignPtrcastForeignPtrtouchForeignPtrnewForeignPtr_addForeignPtrFinalizerEnvaddForeignPtrFinalizermallocForeignPtrBytesmallocForeignPtr FinalizerPtrFinalizerEnvPtrForeign.C.TypesCCharCSCharCUCharCShortCUShortCIntCUIntCLongCULongCLLongCULLongCFloatCDoubleCPtrdiffCSizeCWchar CSigAtomicCClockCTime CUSeconds CSUSecondsCFileCFposCJmpBufCIntPtrCUIntPtrCIntMaxCUIntMaxForeign.Storablepokepeek pokeByteOff peekByteOff pokeElemOff peekElemOff alignmentsizeOfStorablecastPtrToStablePtrcastStablePtrToPtrdeRefStablePtr freeStablePtrcastPtrToFunPtrcastFunPtrToPtr castFunPtr nullFunPtrminusPtralignPtrplusPtrcastPtrnullPtr Data.BitsrotateRrotateLshiftRshiftLisSignedbitSizetestBit complementBitclearBitsetBitbitrotateshift complementxor.|..&.BitswithCStringLenIntConvpeekCStringLenIntConvFaIdxPtrFaIdxInt SamFilePtr SamFileInt BamIterPtr BamIterInt BamFetchFPtr BamIndexPtr BamIndexIntBam1PtrBam1IntBamCigar unBamCigarBamFlag unBamFlag BamHeaderPtr BamHeaderInt BamFilePtr BamFileInt TamFilePtr TamFileInt faiFetchSeq'_ faiDestroy'_ faiLoad'_ sbamWrite'_ sbamRead'_ sbamClose'_ sbamOpen'_bamIterDestroy'_ bamIterRead'_bamIterQuery'_ bamFetch'_bamIndexDestroy'_bamIndexLoad'_ bamFormat1'_ bamDup1'_ bamDestroy1'_ bamInit1'_ bamAux2i'_ bamAux2Z'_ bamAuxGet'_ bamWrite1'_ bamRead1'_bamInitHeaderHash'_bamHeaderWrite'_bamHeaderRead'_bamHeaderDestroy'_bamHeaderInit'_ bamGetTid'_samHeaderRead'_samHeaderRead2'_ samRead1'_ samClose'_ samOpen'_ bam1Seqi'_ bam1Qual'_ bam1Seq'_ bam1QName'_ bam1Cigar'_ bam1MStrand'_ bam1Strand'_bam_cigar_length bam_cigar_opbam_cpadbam_chard_clipbam_csoft_clip bam_cref_skipbam_cdelbam_cins bam_cmatchbam_fdup bam_fqcfailbam_fsecondary bam_fread2 bam_fread1 bam_fmreverse bam_freverse bam_fmunmap bam_funmapbam_fproper_pair bam_fpaired bamClose'_ bamOpen'_mkBamFetchFPtrbamDestroy1PtrbamHeaderDestroyPtrbamOpenbamClose getNTargets setNTargets getTargetName setTargetName getTargetLen setTargetLen flagPairedflagProperPair flagUnmap flagMUnmap flagReverse flagMReverse flagRead1 flagRead2 flagSecondary flagQCFailflagDup cigarMatchcigarInscigarDel cigarRefSkip cigarSoftClip cigarHardClipcigarPadcigarOp cigarLengthgetTIDgetPosgetFlag getNCigargetLQSeqgetMTIDgetMPosgetISize bam1Strand bam1MStrand bam1Cigar bam1QNamebam1Seqbam1Qualbam1SeqisamOpensamClosesamRead1samHeaderRead2 samHeaderRead bamGetTid bamHeaderInitbamHeaderDestroy bamHeaderReadbamHeaderWritebamInitHeaderHashbamRead1 bamWrite1 bamAuxGetbamAux2ZbamAux2ibamInit1 bamDestroy1bamDup1 bamFormat1 bamIndexLoadbamIndexDestroybamFetch bamIterQuery bamIterReadbamIterDestroy getSbamHeadersbamOpen sbamClosesbamRead sbamWritefaiLoad faiDestroy faiFetchSeq packCString useAsCStringfaidx finalizeFaIdx fetchContigptrBam1headerunHeader newHeader cigarTypes toCigarTypemergeAdj outFilenameoutfile inFilenamesamfile Data.MaybeJustNothing isFlagSet seqiToChar newInHandlefinalizeSamFile newOutHandleiterbamindexfinalizeBamIndexfinalizeBamIter