m]      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdef+Instance for special casing null pointers. ghi;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. jIntegral conversion kFloating conversion lObtain C value from Haskell m. nObtain Haskell m from C value. o$Convert a C enumeration to Haskell. p$Convert a Haskell enumeration to C. Vqrstuvwxyz{|}~      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~]^_`abcdefghijklnop]^_`abcdefghijklnop      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZf     !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXf     !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWX 'Input handle for an indexed fasta file [Name of the fasta file \Open an indexed fasta file ]BFetch a region specified by sequence name and coordinates, or the . empty string when the sequence is not found. Sequence name &(Starting, ending) position, 0-based ^ SAM/BAM format alignment _`a *Target sequences from a SAM alignment set bc =Information about one target sequence in a SAM alignment set Target sequence name Target sequence lengh dNumber of target sequences %Returns the list of target sequences :Returns a target sequence by ID, which is a 0-based index %Returns a target sequence name by ID _`a bc d_`a_`a bcbc  dCigar entry including length Cigar entry types Deletion from padded reference 'Trimmed nucleotides, removed from read +Trimmed nucleotides, still present in read &Skipped reference bases, i.e., splice )Deletion from read relative to reference (Insertion in read relative to reference /Aligned nucleotide, may be a match or mismatch ef  Convert a BAM binary cigar integer to a  !g" !" !" !";#Handle for writing SAM/BAM format alignments hij$'Target sequence set for the alignments %Handle for reading SAM/BAM format alignments klm&'Target sequence set for the alignments 'n8 the reference target sequence ID in the target set, or  o for an unmapped read (n the target sequence name, or o for an unmapped  read )n- the total length of the target sequence, or o for  an unmapped read *n; the 0-based index of the leftmost aligned position on the  target sequence, or o for an unmapped read p+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 8n& the length of the query sequence, or o when it is  unavailable. 9n the query sequence, or o when it is unavailable :n the query qualities, or o when it is 8 unavailable. These are returned in ASCII format, i.e., q + 33. q;n6 the target ID of the mate alignment target reference  sequence, or o* when the mate is unmapped or the read is  unpaired. <n; the name of the mate alignment target reference sequence,  or o4 when the mate is unmapped or the read is unpaired. =n3 the length of the mate alignment target reference  sequence, or o* 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 o when the read is # unpaired or the mate is unmapped. ?n the total insert length, or o 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. @n* the match descriptor alignment field, or o when it  is absent An' the number of reported alignments, or o when this  information is not present. Bn/ the number of mismatches in the alignemnt, or o & when this information is not present Cn0 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 o. Dn) the reference sequence location (as per C) on  the target reference (as per () rE1Open 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 sH 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 tMOpen a TAM format file with @SQ headers for writing alignments N.Open a BAM format file for writing alignments O!Close an alignment output handle PQR)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:;<=>?@ABCDEFGHIJKLMNOPQR> '()*+,-./0123456789:;<=>?BA@CD%&&EFGHIJKL#$$MNOPQR0#$$%&&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSuTvU@Handle for fetching alignments by region from a sorted, indexed  BAM file. wV%Filename of sorted, indexed BAM file xWTarget sequences X/Open a sorted, indexed BAM file. YyZ[z\ STUVWXYZ[\ UVWVWXYZSTT[\ STTUVWVWXYZ[\{      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\  ]^_`abcdefghijklmnopqrstuvwxpyzv{|v{}v{~v{vwvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv v v v v vvvvvvvvvvvvvvvvvvv v!v"v#v$v%v&v'v(v)v*v+v,v-v.v/v0v1v2v3v4v5v6v7v8v9v:;v:<v:=v:>v:?v:@v:Av:Bv:Cv:Dv:Ev:Fv:Gv:Hv:Iv:Jv:Kv:Lv:Mv:NvOPvOQvORvOSvOTvOUvOVvOWvOXvOYvZ[vZ\vZ]vZ^vZ_vZ`vZavZbvZcvdevdfvdgvdhvdivdjvklvkmvknvkovkpvqrvqsvqtvquvqvvqwvqxvyvzv{v|v}v~vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvwvwvwvwvvvvvvvvvvvvvvvvvvvvvvvvvvvv      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{)|}~vvXZsamtools-0.1.2Bio.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 withBamInFileget1openTamOutFileopenBamOutFilecloseOutHandlewithTamOutFilewithBamOutFileput1QueryqyHandle IdxHandle idxFilename idxHeader withIndexquerynext withIntConv withFloatConv peekIntConv peekFloatConvwithBoolpeekBoolwithEnumpeekEnum nothingIf nothingIfNullcombineBitMaskscontainsBitMaskextractBitMaskscIntConv cFloatConv cFromBoolghc-primGHC.BoolBoolcToBoolcToEnum cFromEnumbase GHC.Stable newStablePtr GHC.TypesIntGHC.IntInt8Int16Int32Int64 StablePtrGHC.WordWord8Word16Word32Word64GHC.PtrPtrFunPtrGHC.ForeignPtr ForeignPtrForeign.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.Allocfree reallocBytesreallocallocaBytesAligned allocaBytesalloca mallocBytesmalloc finalizerFreeForeign.Marshal.Errorvoid throwIfNull throwIfNeg_ throwIfNegthrowIf_throwIfForeign.ForeignPtrmallocForeignPtrArray0mallocForeignPtrArraynewForeignPtrEnvwithForeignPtr newForeignPtr Foreign.Ptr intPtrToPtr ptrToIntPtr wordPtrToPtr ptrToWordPtrWordPtrIntPtrfreeHaskellFunPtrfinalizeForeignPtrcastForeignPtrunsafeForeignPtrToPtrtouchForeignPtrnewForeignPtr_addForeignPtrFinalizerEnvaddForeignPtrFinalizermallocForeignPtrBytesmallocForeignPtr FinalizerPtrFinalizerEnvPtrForeign.C.TypesCCharCSCharCUCharCShortCUShortCIntCUIntCLongCULongCLLongCULLongCFloatCDoubleCPtrdiffCSizeCWchar CSigAtomicCClockCTimeCFileCFposCJmpBufCIntPtrCUIntPtrCIntMaxCUIntMaxForeign.Storablepokepeek pokeByteOff peekByteOff pokeElemOff peekElemOff alignmentsizeOfStorablecastPtrToStablePtrcastStablePtrToPtrdeRefStablePtr freeStablePtrcastPtrToFunPtrcastFunPtrToPtr castFunPtr nullFunPtrminusPtralignPtrplusPtrcastPtrnullPtr Data.BitsrotateRrotateLshiftRshiftLisSignedbitSizetestBit complementBitclearBitsetBitbitrotateshift complementxor.|..&.BitsGHC.IOunsafePerformIOwithCStringLenIntConvpeekCStringLenIntConv 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'_mkBamFetchFPtrbamDestroy1PtrbamHeaderDestroyPtrFaIdxPtrFaIdxInt SamFilePtr SamFileInt BamIterPtr BamIterInt BamFetchFPtr BamIndexPtr BamIndexIntBam1PtrBam1IntBamCigar unBamCigarBamFlag unBamFlag BamHeaderPtr BamHeaderInt BamFilePtr BamFileInt TamFilePtr TamFileIntbamOpenbamClose 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