úÎlgaé_      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^Nonef_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²³´µ¶·¸¹º»¼½¾¿ÀÁÂÃÄf_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²³´µ¶·¸¹º»¼½¾¿ÀÁÂÃÄb_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²³´µ¶·¸¹º»¼½¾¿ÀÁÂÃÄ Safe-Infered'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   Safe-Infered SAM/BAM format alignment *Target sequences from a SAM alignment set =Information about one target sequence in a SAM alignment set Target sequence name Target sequence lengh Number 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 ÅÆÇ ÈÉ ÊËÅÆÇ ÈÉ Ê ÅÆÇ ÈÉ  ÊË Safe-Infered Cigar 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  Convert a BAM binary cigar integer to a   !" !" !" !" Safe-Infered/#Handle for writing SAM/BAM format alignments $'Target sequence set for the alignments %Handle for reading SAM/BAM format alignments &'Target sequence set for the alignments 'Ì8 the reference target sequence ID in the target set, or  Í for an unmapped read (Ì the target sequence name, or Í for an unmapped  read )Ì- the total length of the target sequence, or Í for  an unmapped read *Ì; the 0-based index of the leftmost aligned position on the  target sequence, or Í for an unmapped read +Is the read paired ,RIs the pair properly aligned (usually based on relative orientation and distance) -Is the read unmapped .)Is the read paired and the mate unmapped /Is the fragment'+s reverse complement aligned to the target 0Is the read paired and the mate'+s reverse complement aligned to the target 14Is the fragment from the first read in the template 25Is the fragment from the second read in the template 3$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 8Ì& the length of the query sequence, or Í when it is  unavailable. 9Ì the query sequence, or Í when it is unavailable :Ì the query qualities, or Í when it is 8 unavailable. These are returned in ASCII format, i.e., q + 33. ;Ì6 the target ID of the mate alignment target reference  sequence, or Í* when the mate is unmapped or the read is  unpaired. <Ì; the name of the mate alignment target reference sequence,  or Í4 when the mate is unmapped or the read is unpaired. =Ì3 the length of the mate alignment target reference  sequence, or Í* 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 Í when the read is # unpaired or the mate is unmapped. ?Ì the total insert length, or Í 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. @Ì* the match descriptor alignment field, or Í when it  is absent AÌ' the number of reported alignments, or Í when this  information is not present. BÌ/ the number of mismatches in the alignemnt, or Í & when this information is not present CÌ0 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 Í. DÌ) the reference sequence location (as per C) on  the target reference (as per () E1Open 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 H 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. NOpen 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 S)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. 1#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRS= #$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRS? '()*+,-./0123456789:;<=>?BA@CD%&&EFGHIJKLM#$$NOPQRS/#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRS Safe-InferedV@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. ^ Use a BAM index file to extract  records aligned to a : specific target sequence (chromosome) number and region. TUVWXYZ[\]^ TUVWXYZ[\]^VWXWXYZ[TUU\]^TUVWXYZ[\]^Î      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\  ]^_`abcdefghijkllmnnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²³´µ¶·¸¹º»¼½¾¿ÀÁÂÃÄÅÆÇÈÉÊËÌÊËÍÎsamtools-0.2.1.1Bio.SamTools.FaIdxBio.SamTools.BamBio.SamTools.CigarBio.SamTools.BamIndexBio.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 readBamRegionFaIdxPtrFaIdxInt SamFilePtr SamFileInt BamIterPtr BamIterInt BamFetchFPtr BamIndexPtr BamIndexIntBam1PtrBam1IntBamCigar unBamCigarBamFlag unBamFlag BamHeaderPtr BamHeaderInt BamFilePtr BamFileInt TamFilePtrmkBamFetchFPtrbamDestroy1PtrbamHeaderDestroyPtrbamOpenbamClose 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 faiFetchSeqptrBam1headerunHeader newHeader $fShowBam1base Data.MaybeJustNothing