Index
| ! | Bio.Genocall.Adna |
| $= | Bio.Iteratee, Bio.Bam |
| $== | Bio.Iteratee, Bio.Bam |
| .= | Data.Avro |
| :* | Bio.Bam.Rec, Bio.Bam |
| :-> | Bio.Genocall.Adna |
| <#> | Bio.Util |
| <=< | Bio.Iteratee, Bio.Bam |
| <>< | Bio.Iteratee, Bio.Bam |
| =$ | Bio.Iteratee, Bio.Bam |
| ><> | Bio.Iteratee, Bio.Bam |
| >=> | Bio.Iteratee, Bio.Bam |
| >>> | Bio.Iteratee, Bio.Bam |
| add | Bio.Bam.Regions |
| addInt | Bio.Bam.Regions |
| addPG | Bio.Bam.Header, Bio.Bam |
| adjustE | Bio.Bam.Rec, Bio.Bam |
| alignedLength | Bio.Bam.Rec, Bio.Bam |
| Avro | Data.Avro |
| BamEnumeratee | Bio.Bam.Reader, Bio.Bam |
| BamHeader | |
| 1 (Type/Class) | Bio.Bam.Header, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Header, Bio.Bam |
| BamIndex | |
| 1 (Type/Class) | Bio.Bam.Index, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Index, Bio.Bam |
| BamKey | |
| 1 (Type/Class) | Bio.Bam.Header, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Header, Bio.Bam |
| BamMeta | |
| 1 (Type/Class) | Bio.Bam.Header, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Header, Bio.Bam |
| BamOtherShit | Bio.Bam.Header, Bio.Bam |
| BamRaw | Bio.Bam.Rec, Bio.Bam |
| bamRaw | Bio.Bam.Rec, Bio.Bam |
| BamrawEnumeratee | Bio.Bam.Reader, Bio.Bam |
| BamRec | |
| 1 (Type/Class) | Bio.Bam.Rec, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Rec, Bio.Bam |
| BamSorting | Bio.Bam.Header, Bio.Bam |
| BamSQ | |
| 1 (Type/Class) | Bio.Bam.Header, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Header, Bio.Bam |
| Base | Bio.Bam.Pileup |
| BasePile | Bio.Bam.Pileup |
| BB | |
| 1 (Type/Class) | Bio.Iteratee.Builder |
| 2 (Data Constructor) | Bio.Iteratee.Builder |
| BestCompression | Bio.Iteratee.ZLib |
| BestSpeed | Bio.Iteratee.ZLib |
| BgzfChunk | Bio.Iteratee.Bgzf |
| bgzfEofMarker | Bio.Iteratee.Bgzf |
| Bin | Bio.Bam.Rec, Bio.Bam |
| Block | |
| 1 (Type/Class) | Bio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam |
| 2 (Data Constructor) | Bio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam |
| block_contents | Bio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam |
| block_offset | Bio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam |
| Both | Bio.TwoBit |
| breakE | Bio.Iteratee, Bio.Bam |
| buffer | Bio.Iteratee.Builder |
| BufferError | Bio.Iteratee.ZLib |
| bump | Bio.Bam.Pileup |
| b_cigar | Bio.Bam.Rec, Bio.Bam |
| b_exts | Bio.Bam.Rec, Bio.Bam |
| b_flag | Bio.Bam.Rec, Bio.Bam |
| b_isize | Bio.Bam.Rec, Bio.Bam |
| b_mapq | Bio.Bam.Rec, Bio.Bam |
| b_mpos | Bio.Bam.Rec, Bio.Bam |
| b_mrnm | Bio.Bam.Rec, Bio.Bam |
| b_pos | Bio.Bam.Rec, Bio.Bam |
| b_qname | Bio.Bam.Rec, Bio.Bam |
| b_qual | Bio.Bam.Rec, Bio.Bam |
| b_rname | Bio.Bam.Rec, Bio.Bam |
| b_seq | Bio.Bam.Rec, Bio.Bam |
| b_virtual_offset | Bio.Bam.Rec, Bio.Bam |
| c2w | Bio.Base, Bio.TwoBit |
| called_sites | Bio.Genocall.AvroFile |
| Calls | Bio.Bam.Pileup |
| CallStats | |
| 1 (Type/Class) | Bio.Bam.Pileup |
| 2 (Data Constructor) | Bio.Bam.Pileup |
| cancelAll | Bio.Iteratee, Bio.Bam |
| cast | Data.Avro |
| Char | Bio.Bam.Rec, Bio.Bam |
| cheap_collapse | Bio.Bam.Rmdup |
| cheap_collapse_keep | Bio.Bam.Rmdup |
| checkErr | Bio.Iteratee, Bio.Bam |
| check_sort | Bio.Bam.Rmdup |
| choose | Bio.Util |
| Chunk | Bio.Iteratee, Bio.Bam |
| Cigar | Bio.Bam.Rec, Bio.Bam |
| CigOp | Bio.Bam.Rec, Bio.Bam |
| clampPosition | Bio.TwoBit |
| Collapse | Bio.Bam.Rmdup |
| combineCoordinates | Bio.Bam.Reader, Bio.Bam |
| combineNames | Bio.Bam.Reader, Bio.Bam |
| compareNames | Bio.Bam.Header, Bio.Bam |
| compl | Bio.Base, Bio.TwoBit |
| complexEntropy | Bio.Bam.Filter, Bio.Bam |
| complexSimple | Bio.Bam.Filter, Bio.Bam |
| compls | Bio.Base, Bio.TwoBit |
| compressBgzf | Bio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam |
| compressBgzf' | Bio.Iteratee.Bgzf |
| compressBgzfLv | Bio.Iteratee.Bgzf |
| compressBufferSize | Bio.Iteratee.ZLib |
| compressChunk | Bio.Iteratee.Bgzf |
| compressDictionary | Bio.Iteratee.ZLib |
| CompressionLevel | |
| 1 (Type/Class) | Bio.Iteratee.ZLib |
| 2 (Data Constructor) | Bio.Iteratee.ZLib |
| CompressionStrategy | Bio.Iteratee.ZLib |
| compression_level | Bio.Iteratee.Bgzf |
| compressLevel | Bio.Iteratee.ZLib |
| compressMemoryLevel | Bio.Iteratee.ZLib |
| compressMethod | Bio.Iteratee.ZLib |
| CompressParams | |
| 1 (Type/Class) | Bio.Iteratee.Bgzf |
| 2 (Data Constructor) | Bio.Iteratee.Bgzf |
| 3 (Type/Class) | Bio.Iteratee.ZLib |
| 4 (Data Constructor) | Bio.Iteratee.ZLib |
| compressStrategy | Bio.Iteratee.ZLib |
| compressWindowBits | Bio.Iteratee.ZLib |
| concatDefaultInputs | Bio.Bam.Reader, Bio.Bam |
| concatInputs | Bio.Bam.Reader, Bio.Bam |
| concatMapStream | Bio.Iteratee, Bio.Bam |
| concatMapStreamM | Bio.Iteratee, Bio.Bam |
| consume_active | Bio.Bam.Pileup |
| cons_collapse | Bio.Bam.Rmdup |
| cons_collapse_keep | Bio.Bam.Rmdup |
| ContainerOpts | |
| 1 (Type/Class) | Data.Avro |
| 2 (Data Constructor) | Data.Avro |
| convStream | Bio.Iteratee, Bio.Bam |
| Coordinate | Bio.Bam.Header, Bio.Bam |
| DamagedBase | Bio.Bam.Pileup |
| DamageModel | Bio.Genocall.Adna |
| DamageParameters | Bio.Genocall.Adna |
| DataError | Bio.Iteratee.ZLib |
| DataRemaining | Bio.Iteratee, Bio.Bam |
| DB | Bio.Bam.Pileup |
| db_call | Bio.Bam.Pileup |
| db_dmg | Bio.Bam.Pileup |
| db_qual | Bio.Bam.Pileup |
| decodeAnyBam | Bio.Bam.Reader, Bio.Bam |
| decodeAnyBamFile | Bio.Bam.Reader, Bio.Bam |
| decodeAnyBamOrSam | Bio.Bam.Reader, Bio.Bam |
| decodeAnyBamOrSamFile | Bio.Bam.Reader, Bio.Bam |
| decodeBam | Bio.Bam.Reader, Bio.Bam |
| decodeIntBase128 | Data.Avro |
| decodeSam | Bio.Bam.Reader, Bio.Bam |
| decodeSam' | Bio.Bam.Reader, Bio.Bam |
| decodeWordBase128 | Data.Avro |
| decompose | Bio.Bam.Pileup |
| decompressBgzf | Bio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam |
| decompressBgzfBlocks | Bio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam |
| decompressBgzfBlocks' | Bio.Iteratee.Bgzf |
| decompressBufferSize | Bio.Iteratee.ZLib |
| decompressDictionary | Bio.Iteratee.ZLib |
| DecompressParams | |
| 1 (Type/Class) | Bio.Iteratee.ZLib |
| 2 (Data Constructor) | Bio.Iteratee.ZLib |
| decompressPlain | Bio.Iteratee.Bgzf |
| decompressWindowBits | Bio.Iteratee.ZLib |
| defaultBufSize | Bio.Iteratee, Bio.Bam |
| DefaultCompression | Bio.Iteratee.ZLib |
| defaultCompressParams | Bio.Iteratee.ZLib |
| defaultDecompressParams | Bio.Iteratee.ZLib |
| DefaultMemoryLevel | Bio.Iteratee.ZLib |
| DefaultStrategy | Bio.Iteratee.ZLib |
| DefaultWindowBits | Bio.Iteratee.ZLib |
| Deflated | Bio.Iteratee.ZLib |
| Del | Bio.Bam.Rec, Bio.Bam |
| deleted_bases | Bio.Bam.Pileup |
| deleteE | Bio.Bam.Rec, Bio.Bam |
| deletePQ | Bio.PriorityQueue |
| depth | Bio.Bam.Index, Bio.Bam |
| dequeuePQ | Bio.PriorityQueue |
| deriveAvro | Data.Avro |
| deriveAvros | Data.Avro |
| displayException | Bio.Iteratee, Bio.Bam |
| distinctBin | Bio.Bam.Header, Bio.Bam |
| DivergentException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| doubleToWord | Data.Avro |
| DP | Bio.Genocall.Adna |
| dropStream | Bio.Iteratee, Bio.Bam |
| dsd_delta | Bio.Genocall.Adna |
| dsd_lambda | Bio.Genocall.Adna |
| dsd_sigma | Bio.Genocall.Adna |
| eflagMerged | Bio.Bam.Header, Bio.Bam |
| eflagTrimmed | Bio.Bam.Header, Bio.Bam |
| Empty | Bio.Bam.Pileup |
| empty | Bio.Iteratee, Bio.Bam |
| emptyQ | Bio.Iteratee, Bio.Bam |
| encodeBamWith | Bio.Bam.Writer, Bio.Bam |
| encodeBgzfWith | Bio.Iteratee.Builder |
| encodeIntBase128 | Data.Avro |
| encodeWordBase128 | Data.Avro |
| end | Bio.Bam.Regions, Bio.Bam.Index, Bio.Bam |
| Endian | Bio.Iteratee, Bio.Bam |
| endianRead2 | Bio.Iteratee, Bio.Bam |
| endianRead3 | Bio.Iteratee, Bio.Bam |
| endianRead3i | Bio.Iteratee, Bio.Bam |
| endianRead4 | Bio.Iteratee, Bio.Bam |
| endianRead8 | Bio.Iteratee, Bio.Bam |
| EndOfRead | Bio.Bam.Pileup |
| endRecord | Bio.Iteratee.Builder |
| eneeBamRefseq | Bio.Bam.Index, Bio.Bam |
| eneeBamRegions | Bio.Bam.Index, Bio.Bam |
| eneeBamSubseq | Bio.Bam.Index, Bio.Bam |
| eneeBamUnaligned | Bio.Bam.Index, Bio.Bam |
| eneeCheckIfDone | Bio.Iteratee, Bio.Bam |
| eneeCheckIfDoneHandle | Bio.Iteratee, Bio.Bam |
| eneeCheckIfDoneIgnore | Bio.Iteratee, Bio.Bam |
| eneeCheckIfDonePass | Bio.Iteratee, Bio.Bam |
| enee_glf_file | Bio.Glf |
| enqueuePQ | Bio.PriorityQueue |
| enStrExc | Bio.Iteratee, Bio.Bam |
| ensureBuffer | Bio.Iteratee.Builder |
| enumAuxFile | Bio.Iteratee, Bio.Bam |
| enumBlockFlush | Bio.Iteratee.ZLib |
| enumCheckIfDone | Bio.Iteratee, Bio.Bam |
| enumChunk | Bio.Iteratee, Bio.Bam |
| enumDefaultInputs | Bio.Iteratee, Bio.Bam |
| enumDeflate | Bio.Iteratee.ZLib |
| enumEof | Bio.Iteratee, Bio.Bam |
| Enumeratee | Bio.Iteratee, Bio.Bam |
| Enumeratee' | Bio.Iteratee, Bio.Bam |
| EnumerateeHandler | Bio.Iteratee, Bio.Bam |
| Enumerator | Bio.Iteratee, Bio.Bam |
| Enumerator' | Bio.Iteratee, Bio.Bam |
| enumErr | Bio.Iteratee, Bio.Bam |
| EnumException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| enumFd | Bio.Iteratee, Bio.Bam |
| enumFdRandom | Bio.Iteratee, Bio.Bam |
| enumFile | Bio.Iteratee, Bio.Bam |
| enumFileRandom | Bio.Iteratee, Bio.Bam |
| enumFromCallback | Bio.Iteratee, Bio.Bam |
| enumFromCallbackCatch | Bio.Iteratee, Bio.Bam |
| enumFullFlush | Bio.Iteratee.ZLib |
| enumHandle | Bio.Iteratee, Bio.Bam |
| enumHandleRandom | Bio.Iteratee, Bio.Bam |
| enumInflate | Bio.Iteratee.ZLib |
| enumInflateAny | Bio.Iteratee.ZLib |
| enumInputs | Bio.Iteratee, Bio.Bam |
| enumLines | Bio.Iteratee, Bio.Bam |
| enumLinesBS | Bio.Iteratee, Bio.Bam |
| enumList | Bio.Iteratee, Bio.Bam |
| enumPure1Chunk | Bio.Iteratee, Bio.Bam |
| EnumStringException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| enumSyncFlush | Bio.Iteratee.ZLib |
| EnumUnhandledIterException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| enumWords | Bio.Iteratee, Bio.Bam |
| enumWordsBS | Bio.Iteratee, Bio.Bam |
| enum_glf_file | Bio.Glf |
| enum_glf_handle | Bio.Glf |
| EOF | Bio.Iteratee, Bio.Bam |
| EofError | Bio.Iteratee, Bio.Bam |
| EofException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| EofNoError | Bio.Iteratee, Bio.Bam |
| Equal | Bio.Iteratee, Bio.Bam |
| errorContexts | Bio.Iteratee, Bio.Bam |
| errorMessage | Bio.Iteratee, Bio.Bam |
| estimateComplexity | Bio.Util |
| everything | Bio.Base, Bio.TwoBit |
| Exception | Bio.Iteratee, Bio.Bam |
| expandBuffer | Bio.Iteratee.Builder |
| expm1 | Bio.Util |
| Ext | Bio.Bam.Rec, Bio.Bam |
| extAsInt | Bio.Bam.Rec, Bio.Bam |
| extAsString | Bio.Bam.Rec, Bio.Bam |
| extendRange | Bio.Base, Bio.TwoBit |
| Extensions | Bio.Bam.Rec, Bio.Bam |
| extensions | Bio.Bam.Index, Bio.Bam |
| Fd | Bio.Iteratee, Bio.Bam |
| fileDriver | Bio.Iteratee, Bio.Bam |
| fileDriverRandom | Bio.Iteratee, Bio.Bam |
| fileDriverRandomVBuf | Bio.Iteratee, Bio.Bam |
| fileDriverVBuf | Bio.Iteratee, Bio.Bam |
| FileOffset | Bio.Iteratee, Bio.Bam |
| filetype_label | Data.Avro |
| Filtered | Bio.Iteratee.ZLib |
| filterPairs | Bio.Bam.Filter, Bio.Bam |
| filterStream | Bio.Iteratee, Bio.Bam |
| filterStreamM | Bio.Iteratee, Bio.Bam |
| findAuxFile | Bio.Base, Bio.TwoBit |
| fixupBwaFlags | Bio.Bam.Evan |
| fixupFlagAbuse | Bio.Bam.Evan |
| flagAuxillary | Bio.Bam.Header, Bio.Bam |
| flagDuplicate | Bio.Bam.Header, Bio.Bam |
| flagFailsQC | Bio.Bam.Header, Bio.Bam |
| flagFirstMate | Bio.Bam.Header, Bio.Bam |
| flagMateReversed | Bio.Bam.Header, Bio.Bam |
| flagMateUnmapped | Bio.Bam.Header, Bio.Bam |
| flagPaired | Bio.Bam.Header, Bio.Bam |
| flagProperlyPaired | Bio.Bam.Header, Bio.Bam |
| flagReversed | Bio.Bam.Header, Bio.Bam |
| flagSecondMate | Bio.Bam.Header, Bio.Bam |
| flagUnmapped | Bio.Bam.Header, Bio.Bam |
| Float | Bio.Bam.Rec, Bio.Bam |
| float2mini | Bio.Util |
| FloatArr | Bio.Bam.Rec, Bio.Bam |
| floatToWord | Data.Avro |
| foldChunksM | Bio.Iteratee, Bio.Bam |
| foldStream | Bio.Iteratee, Bio.Bam |
| foldStreamM | Bio.Iteratee, Bio.Bam |
| Format | Bio.Iteratee.ZLib |
| fromBin | Data.Avro |
| fromException | Bio.Iteratee, Bio.Bam |
| fromIterException | Bio.Iteratee, Bio.Bam |
| fromList | Bio.Bam.Regions |
| fromProb | Bio.Base, Bio.TwoBit |
| fromQual | Bio.Base, Bio.TwoBit |
| fromQualRaised | Bio.Base, Bio.TwoBit |
| gap | Bio.Base, Bio.TwoBit |
| GenoCallBlock | |
| 1 (Type/Class) | Bio.Genocall.AvroFile |
| 2 (Data Constructor) | Bio.Genocall.AvroFile |
| GenoCallSite | |
| 1 (Type/Class) | Bio.Genocall.AvroFile |
| 2 (Data Constructor) | Bio.Genocall.AvroFile |
| genSubstMat | Bio.Genocall.Adna |
| getBamRaw | Bio.Bam.Reader, Bio.Bam |
| getChunk | Bio.Iteratee, Bio.Bam |
| getChunks | Bio.Iteratee, Bio.Bam |
| getMd | Bio.Bam.Rec, Bio.Bam |
| getMinKey | Bio.Bam.Pileup |
| getMinPQ | Bio.PriorityQueue |
| getOffset | Bio.Iteratee.Bgzf |
| getRandomSeq | Bio.TwoBit |
| getRef | Bio.Bam.Header, Bio.Bam |
| getSeqLength | Bio.TwoBit |
| getSeqnames | Bio.TwoBit |
| getSubseq | Bio.TwoBit |
| getSubseqAscii | Bio.TwoBit |
| getSubseqMasked | Bio.TwoBit |
| getSubseqWith | Bio.TwoBit |
| get_active | Bio.Bam.Pileup |
| get_damage_model | Bio.Bam.Pileup |
| get_pos | Bio.Bam.Pileup |
| get_refseq | Bio.Bam.Pileup |
| get_waiting | Bio.Bam.Pileup |
| GL | Bio.Bam.Pileup |
| GlfRec | Bio.Glf |
| GlfSeq | |
| 1 (Type/Class) | Bio.Glf |
| 2 (Data Constructor) | Bio.Glf |
| glf_depth | Bio.Glf |
| glf_is_ins1 | Bio.Glf |
| glf_is_ins2 | Bio.Glf |
| glf_lk | Bio.Glf |
| glf_lk_het | Bio.Glf |
| glf_lk_hom1 | Bio.Glf |
| glf_lk_hom2 | Bio.Glf |
| glf_mapq | Bio.Glf |
| glf_min_lk | Bio.Glf |
| glf_offset | Bio.Glf |
| glf_refbase | Bio.Glf |
| glf_seq1 | Bio.Glf |
| glf_seq2 | Bio.Glf |
| glf_seqlen | Bio.Glf |
| glf_seqname | Bio.Glf |
| Globally | Bio.Align |
| Grouped | Bio.Bam.Header, Bio.Bam |
| GroupSorted | Bio.Bam.Header, Bio.Bam |
| groupStreamBy | Bio.Iteratee, Bio.Bam |
| groupStreamOn | Bio.Iteratee, Bio.Bam |
| GZip | Bio.Iteratee.ZLib |
| GZipOrZlib | Bio.Iteratee.ZLib |
| Hard | Bio.TwoBit |
| HasPrefix | Bio.Align |
| hasSequence | Bio.TwoBit |
| hdr_other_shit | Bio.Bam.Header, Bio.Bam |
| hdr_sorting | Bio.Bam.Header, Bio.Bam |
| hdr_version | Bio.Bam.Header, Bio.Bam |
| heads | Bio.Iteratee, Bio.Bam |
| headStream | Bio.Iteratee, Bio.Bam |
| Heap | Bio.Bam.Pileup |
| HMa | Bio.Bam.Rec, Bio.Bam |
| HuffmanOnly | Bio.Iteratee.ZLib |
| icont | Bio.Iteratee, Bio.Bam |
| icontM | Bio.Iteratee, Bio.Bam |
| idone | Bio.Iteratee, Bio.Bam |
| idoneM | Bio.Iteratee, Bio.Bam |
| IException | Bio.Iteratee, Bio.Bam |
| IFException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| ifold | Bio.Iteratee, Bio.Bam |
| iGetString | Bio.Iteratee, Bio.Bam |
| ilift | Bio.Iteratee, Bio.Bam |
| iLookAhead | Bio.Iteratee, Bio.Bam |
| IncorrectCompressionLevel | Bio.Iteratee.ZLib |
| IncorrectMemoryLevel | Bio.Iteratee.ZLib |
| IncorrectState | Bio.Iteratee.ZLib |
| IncorrectWindowBits | Bio.Iteratee.ZLib |
| Indel | |
| 1 (Data Constructor) | Bio.Glf |
| 2 (Data Constructor) | Bio.Bam.Pileup |
| IndelPile | Bio.Bam.Pileup |
| IndelVariant | |
| 1 (Type/Class) | Bio.Bam.Pileup |
| 2 (Data Constructor) | Bio.Bam.Pileup |
| indel_likelihoods | Bio.Genocall.AvroFile |
| indel_stats | Bio.Genocall.AvroFile |
| indel_variants | Bio.Genocall.AvroFile |
| Ins | Bio.Bam.Rec, Bio.Bam |
| insert | Bio.Bam.Pileup |
| insertE | Bio.Bam.Rec, Bio.Bam |
| inserted_bases | Bio.Bam.Pileup |
| insideRange | Bio.Base, Bio.TwoBit |
| Int | Bio.Bam.Rec, Bio.Bam |
| IntArr | Bio.Bam.Rec, Bio.Bam |
| invalidPos | Bio.Bam.Header, Bio.Bam |
| invalidRefseq | Bio.Bam.Header, Bio.Bam |
| invnormcdf | Bio.Util |
| ioBind | Bio.Iteratee, Bio.Bam |
| ioBind_ | Bio.Iteratee, Bio.Bam |
| isAuxillary | Bio.Bam.Rec, Bio.Bam |
| isBam | Bio.Bam.Reader, Bio.Bam |
| isBamOrSam | Bio.Bam.Reader, Bio.Bam |
| IsBamRec | Bio.Bam.Writer, Bio.Bam |
| isBase | Bio.Base, Bio.TwoBit |
| isBgzf | Bio.Iteratee.Bgzf |
| isBgzfBam | Bio.Bam.Reader, Bio.Bam |
| isDuplicate | Bio.Bam.Rec, Bio.Bam |
| isFailsQC | Bio.Bam.Rec, Bio.Bam |
| isFinished | Bio.Iteratee, Bio.Bam |
| isFirstMate | Bio.Bam.Rec, Bio.Bam |
| isGap | Bio.Base, Bio.TwoBit |
| isGzip | Bio.Iteratee.Bgzf |
| isGzipBam | Bio.Bam.Reader, Bio.Bam |
| isKnownMapq | Bio.Bam.Header, Bio.Bam |
| isMateReversed | Bio.Bam.Rec, Bio.Bam |
| isMateUnmapped | Bio.Bam.Rec, Bio.Bam |
| isMerged | Bio.Bam.Rec, Bio.Bam |
| isPaired | Bio.Bam.Rec, Bio.Bam |
| isPlainBam | Bio.Bam.Reader, Bio.Bam |
| IsPrefix | Bio.Align |
| isProperBase | Bio.Base, Bio.TwoBit |
| isProperlyPaired | Bio.Bam.Rec, Bio.Bam |
| isReversed | Bio.Bam.Rec, Bio.Bam |
| isSecondMate | Bio.Bam.Rec, Bio.Bam |
| isStreamFinished | Bio.Iteratee, Bio.Bam |
| isTrimmed | Bio.Bam.Rec, Bio.Bam |
| isUnmapped | Bio.Bam.Rec, Bio.Bam |
| isValidPos | Bio.Bam.Header, Bio.Bam |
| isValidRefseq | Bio.Bam.Header, Bio.Bam |
| Iteratee | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| IterException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| iterExceptionFromException | Bio.Iteratee, Bio.Bam |
| iterExceptionToException | Bio.Iteratee, Bio.Bam |
| iterGet | Data.Avro |
| iterLoop | Data.Avro |
| iterStrExc | Bio.Iteratee, Bio.Bam |
| IterStringException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| joinI | Bio.Iteratee, Bio.Bam |
| joinIM | Bio.Iteratee, Bio.Bam |
| LeftoverChunk | Bio.Iteratee.Bgzf |
| len | Bio.Iteratee.Builder |
| lengthQ | Bio.Iteratee, Bio.Bam |
| Less | Bio.Iteratee, Bio.Bam |
| lift | Bio.Iteratee, Bio.Bam |
| liftBlock | Bio.Iteratee.Bgzf |
| liftI | Bio.Iteratee, Bio.Bam |
| liftIO | Bio.Iteratee, Bio.Bam |
| ListLike | Bio.Iteratee, Bio.Bam |
| lMap | Bio.Iteratee, Bio.Bam |
| log1p | Bio.Util |
| lookupLT | Bio.Bam.Regions |
| LooseMap | Bio.Iteratee, Bio.Bam |
| LSB | Bio.Iteratee, Bio.Bam |
| makePQ | Bio.PriorityQueue |
| mapChunks | Bio.Iteratee, Bio.Bam |
| mapChunksM | Bio.Iteratee, Bio.Bam |
| mapChunksM_ | Bio.Iteratee, Bio.Bam |
| mapIteratee | Bio.Iteratee, Bio.Bam |
| mapMaybeStream | Bio.Iteratee, Bio.Bam |
| mapStream | Bio.Iteratee, Bio.Bam |
| mapStreamM | Bio.Iteratee, Bio.Bam |
| mapStreamM_ | Bio.Iteratee, Bio.Bam |
| maq_snp_call | Bio.Genocall |
| mark | Bio.Iteratee.Builder |
| Mask | Bio.TwoBit |
| Mat | Bio.Bam.Rec, Bio.Bam |
| maxBlockSize | Bio.Iteratee.Bgzf |
| MaxMemoryLevel | Bio.Iteratee.ZLib |
| max_mb | Bio.PriorityQueue |
| mBind | Bio.Iteratee, Bio.Bam |
| mBind_ | Bio.Iteratee, Bio.Bam |
| MdDel | Bio.Bam.Header, Bio.Bam |
| MdNum | Bio.Bam.Header, Bio.Bam |
| MdOp | Bio.Bam.Header, Bio.Bam |
| MdRep | Bio.Bam.Header, Bio.Bam |
| memoDamageModel | Bio.Genocall.Adna |
| memoObject | Data.Avro |
| MemoryError | Bio.Iteratee.ZLib |
| MemoryLevel | |
| 1 (Type/Class) | Bio.Iteratee.ZLib |
| 2 (Data Constructor) | Bio.Iteratee.ZLib |
| mergeDefaultInputs | Bio.Bam.Reader, Bio.Bam |
| mergeEnums | Bio.Iteratee, Bio.Bam |
| mergeEnums' | Bio.Iteratee, Bio.Bam |
| mergeInputs | Bio.Bam.Reader, Bio.Bam |
| mergeSortStreams | Bio.Iteratee, Bio.Bam |
| meta_comment | Bio.Bam.Header, Bio.Bam |
| meta_hdr | Bio.Bam.Header, Bio.Bam |
| meta_other_shit | Bio.Bam.Header, Bio.Bam |
| meta_refs | Bio.Bam.Header, Bio.Bam |
| Method | Bio.Iteratee.ZLib |
| mini2float | Bio.Util |
| MinMemoryLevel | Bio.Iteratee.ZLib |
| minshift | Bio.Bam.Index, Bio.Bam |
| MkSchema | |
| 1 (Type/Class) | Data.Avro |
| 2 (Data Constructor) | Data.Avro |
| mkSchema | Data.Avro |
| mk_snp_gts | Bio.Genocall |
| Mode | Bio.Align |
| MonadIO | Bio.Iteratee, Bio.Bam |
| MonadMask | Bio.Iteratee, Bio.Bam |
| MSB | Bio.Iteratee, Bio.Bam |
| myersAlign | Bio.Align |
| N | Bio.Base, Bio.TwoBit |
| NeedDictionary | Bio.Iteratee.ZLib |
| newBuffer | Bio.Iteratee.Builder |
| NoChunk | Bio.Iteratee.Bgzf |
| NoCompression | Bio.Iteratee.ZLib |
| noDamage | Bio.Genocall.Adna |
| Node | Bio.Bam.Pileup |
| None | Bio.TwoBit |
| Nop | Bio.Bam.Rec, Bio.Bam |
| noRefs | Bio.Bam.Header, Bio.Bam |
| normalizeTo | Bio.Bam.Rmdup |
| NotLess | Bio.Iteratee, Bio.Bam |
| Ns | Bio.Base, Bio.Bam.Rec, Bio.Bam, Bio.TwoBit |
| nucA | Bio.Base, Bio.TwoBit |
| nucC | Bio.Base, Bio.TwoBit |
| nucG | Bio.Base, Bio.TwoBit |
| Nucleotide | Bio.Base, Bio.TwoBit |
| Nucleotides | Bio.Base, Bio.Bam.Rec, Bio.Bam, Bio.TwoBit |
| nucsA | Bio.Base, Bio.TwoBit |
| nucsC | Bio.Base, Bio.TwoBit |
| nucsG | Bio.Base, Bio.TwoBit |
| nucsN | Bio.Base, Bio.TwoBit |
| nucsT | Bio.Base, Bio.TwoBit |
| nucT | Bio.Base, Bio.TwoBit |
| nucToNucs | Bio.Base, Bio.TwoBit |
| Nullable | Bio.Iteratee, Bio.Bam |
| nullBamRec | Bio.Bam.Rec, Bio.Bam |
| nullC | Bio.Iteratee, Bio.Bam |
| NullPoint | Bio.Iteratee, Bio.Bam |
| objects_per_block | Data.Avro |
| openTwoBit | Bio.TwoBit |
| Ordering' | Bio.Iteratee, Bio.Bam |
| overlaps | Bio.Bam.Regions |
| packSeqid | Bio.Base, Bio.TwoBit |
| Pad | Bio.Bam.Rec, Bio.Bam |
| parMapChunksIO | Bio.Iteratee, Bio.Iteratee.Bgzf, Bio.Bam |
| parseBamMeta | Bio.Bam.Header, Bio.Bam |
| parseBamMetaLine | Bio.Bam.Header, Bio.Bam |
| ParseError | |
| 1 (Type/Class) | Bio.Iteratee, Bio.Bam |
| 2 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| parseFastq | Bio.Bam.Fastq, Bio.Bam |
| parseFastq' | Bio.Bam.Fastq, Bio.Bam |
| parseFastqCassava | Bio.Bam.Fastq, Bio.Bam |
| parserToIteratee | Bio.Iteratee, Bio.Bam |
| partitionPairEithers | Bio.Bam.Pileup |
| peek | Bio.Bam.Pileup |
| peekMinPQ | Bio.PriorityQueue |
| peekStream | Bio.Iteratee, Bio.Bam |
| phredconverse | Bio.Util |
| phredminus | Bio.Util |
| phredplus | Bio.Util |
| phredsum | Bio.Util |
| Pile | |
| 1 (Type/Class) | Bio.Bam.Pileup |
| 2 (Data Constructor) | Bio.Bam.Pileup |
| Pile' | Bio.Bam.Pileup |
| PileF | Bio.Bam.Pileup |
| PileM | |
| 1 (Type/Class) | Bio.Bam.Pileup |
| 2 (Data Constructor) | Bio.Bam.Pileup |
| pileup | Bio.Bam.Pileup |
| pileup' | Bio.Bam.Pileup |
| pileup'' | Bio.Bam.Pileup |
| pipeBamOutput | Bio.Bam.Writer, Bio.Bam |
| pipeSamOutput | Bio.Bam.Writer, Bio.Bam |
| popQ | Bio.Iteratee, Bio.Bam |
| Pos | Bio.Base, Bio.TwoBit |
| Position | Bio.Base, Bio.TwoBit |
| pow | Bio.Base, Bio.TwoBit |
| PQ | Bio.PriorityQueue |
| PQ_Conf | |
| 1 (Type/Class) | Bio.PriorityQueue |
| 2 (Data Constructor) | Bio.PriorityQueue |
| Pr | Bio.Base, Bio.TwoBit |
| PrimBase | Bio.Bam.Pileup |
| PrimChunks | Bio.Bam.Pileup |
| printLines | Bio.Iteratee, Bio.Bam |
| printLinesUnterminated | Bio.Iteratee, Bio.Bam |
| Prob | Bio.Base, Bio.TwoBit |
| probToQual | Bio.Base, Bio.TwoBit |
| progressNum | Bio.Iteratee, Bio.Bam |
| progressPos | Bio.Bam.Rec, Bio.Bam |
| properBases | Bio.Base, Bio.TwoBit |
| protectTerm | Bio.Iteratee, Bio.Bam |
| Push | |
| 1 (Type/Class) | Bio.Iteratee.Builder |
| 2 (Data Constructor) | Bio.Iteratee.Builder |
| pushBam | Bio.Bam.Writer, Bio.Bam |
| pushBuilder | Bio.Iteratee.Builder |
| pushByte | Bio.Iteratee.Builder |
| pushByteString | Bio.Iteratee.Builder |
| pushQ | Bio.Iteratee, Bio.Bam |
| pushWord16 | Bio.Iteratee.Builder |
| pushWord32 | Bio.Iteratee.Builder |
| p_indel_pile | Bio.Bam.Pileup |
| p_indel_stat | Bio.Bam.Pileup |
| p_is_reverse | Bio.Base, Bio.TwoBit |
| p_pos | Bio.Bam.Pileup |
| p_refseq | Bio.Bam.Pileup |
| p_seq | Bio.Base, Bio.TwoBit |
| p_snp_pile | Bio.Bam.Pileup |
| p_snp_stat | Bio.Bam.Pileup |
| p_start | Bio.Base, Bio.TwoBit |
| Q | Bio.Base, Bio.TwoBit |
| 1 (Type/Class) | Bio.Iteratee, Bio.Bam |
| 2 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| Qual | Bio.Base, Bio.TwoBit |
| QualFilter | Bio.Bam.Filter, Bio.Bam |
| qualityAverage | Bio.Bam.Filter, Bio.Bam |
| qualityFromNewIllumina | Bio.Bam.Filter, Bio.Bam |
| qualityFromOldIllumina | Bio.Bam.Filter, Bio.Bam |
| qualityMinimum | Bio.Bam.Filter, Bio.Bam |
| qualToProb | Bio.Base, Bio.TwoBit |
| Queryname | Bio.Bam.Header, Bio.Bam |
| queue_depth | Bio.Iteratee.Bgzf |
| Range | |
| 1 (Type/Class) | Bio.Base, Bio.TwoBit |
| 2 (Data Constructor) | Bio.Base, Bio.TwoBit |
| Raw | Bio.Iteratee.ZLib |
| raw_data | Bio.Bam.Rec, Bio.Bam |
| readAvroContainer | Data.Avro |
| readBaiIndex | Bio.Bam.Index, Bio.Bam |
| readBamIndex | Bio.Bam.Index, Bio.Bam |
| readMd | Bio.Bam.Header, Bio.Bam |
| reads_mapq0 | Bio.Bam.Pileup |
| readTabix | Bio.Bam.Index, Bio.Bam |
| readWord16be_bs | Bio.Iteratee, Bio.Bam |
| readWord16le_bs | Bio.Iteratee, Bio.Bam |
| readWord32be_bs | Bio.Iteratee, Bio.Bam |
| readWord32le_bs | Bio.Iteratee, Bio.Bam |
| readWord64be_bs | Bio.Iteratee, Bio.Bam |
| readWord64le_bs | Bio.Iteratee, Bio.Bam |
| read_depth | Bio.Bam.Pileup |
| RecordChunk | Bio.Iteratee.Bgzf |
| reference_name | Bio.Genocall.AvroFile |
| Refs | Bio.Bam.Header, Bio.Bam |
| Refseq | |
| 1 (Type/Class) | Bio.Bam.Header, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Header, Bio.Bam |
| refseq | Bio.Bam.Regions, Bio.Bam.Index, Bio.Bam |
| refseq_bins | Bio.Bam.Index, Bio.Bam |
| refseq_ckpoints | Bio.Bam.Index, Bio.Bam |
| Region | |
| 1 (Type/Class) | Bio.Bam.Regions, Bio.Bam.Index, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Regions, Bio.Bam.Index, Bio.Bam |
| Regions | |
| 1 (Type/Class) | Bio.Bam.Regions |
| 2 (Data Constructor) | Bio.Bam.Regions |
| removeWarts | Bio.Bam.Evan |
| reverseRange | Bio.Base, Bio.TwoBit |
| rmdup | Bio.Bam.Rmdup |
| run | Bio.Iteratee, Bio.Bam |
| runIter | Bio.Iteratee, Bio.Bam |
| runMkSchema | Data.Avro |
| runPileM | Bio.Bam.Pileup |
| r_length | Bio.Base, Bio.TwoBit |
| r_pos | Bio.Base, Bio.TwoBit |
| Seek | Bio.Bam.Pileup |
| seek | Bio.Iteratee, Bio.Bam |
| SeekException | |
| 1 (Data Constructor) | Bio.Iteratee, Bio.Bam |
| 2 (Type/Class) | Bio.Iteratee, Bio.Bam |
| Seqid | Bio.Base, Bio.TwoBit |
| setEOF | Bio.Iteratee, Bio.Bam |
| setMark | Bio.Iteratee.Builder |
| setQualFlag | Bio.Bam.Rec, Bio.Bam |
| set_pos | Bio.Bam.Pileup |
| shiftPosition | Bio.Base, Bio.TwoBit |
| shiftRange | Bio.Base, Bio.TwoBit |
| showAligned | Bio.Align |
| showBamMeta | Bio.Bam.Header, Bio.Bam |
| showMd | Bio.Bam.Header, Bio.Bam |
| showNucleotide | Bio.Base, Bio.TwoBit |
| showNucleotides | Bio.Base, Bio.TwoBit |
| showNum | Bio.Util |
| showOOM | Bio.Util |
| simple_call | Bio.Genocall |
| simple_indel_call | Bio.Genocall |
| simple_snp_call | Bio.Genocall |
| Sizeable | Bio.PriorityQueue |
| sizePQ | Bio.PriorityQueue |
| skipToEof | Bio.Iteratee, Bio.Bam |
| SMa | Bio.Bam.Rec, Bio.Bam |
| SNP | Bio.Glf |
| snp_likelihoods | Bio.Genocall.AvroFile |
| snp_stats | Bio.Genocall.AvroFile |
| Soft | Bio.TwoBit |
| SpecialChunk | Bio.Iteratee.Bgzf |
| sq_length | Bio.Bam.Header, Bio.Bam |
| sq_name | Bio.Bam.Header, Bio.Bam |
| sq_other_shit | Bio.Bam.Header, Bio.Bam |
| ssd_delta | Bio.Genocall.Adna |
| ssd_kappa | Bio.Genocall.Adna |
| ssd_lambda | Bio.Genocall.Adna |
| ssd_sigma | Bio.Genocall.Adna |
| start | Bio.Bam.Regions, Bio.Bam.Index, Bio.Bam |
| start_position | Bio.Genocall.AvroFile |
| stderr | Bio.Iteratee, Bio.Bam |
| stdin | Bio.Iteratee, Bio.Bam |
| stdout | Bio.Iteratee, Bio.Bam |
| Stream | Bio.Iteratee, Bio.Bam |
| stream2vector | Bio.Iteratee, Bio.Bam |
| stream2vectorN | Bio.Iteratee, Bio.Bam |
| StreamError | Bio.Iteratee.ZLib |
| StreamStatus | Bio.Iteratee, Bio.Bam |
| string | Data.Avro |
| subsampleBam | Bio.Bam.Index, Bio.Bam |
| Subsequence | |
| 1 (Type/Class) | Bio.Bam.Regions, Bio.Bam.Index, Bio.Bam |
| 2 (Data Constructor) | Bio.Bam.Regions, Bio.Bam.Index, Bio.Bam |
| sum_mapq | Bio.Bam.Pileup |
| sum_mapq_squared | Bio.Bam.Pileup |
| takeStream | Bio.Iteratee, Bio.Bam |
| takeWhileE | Bio.Iteratee, Bio.Bam |
| temp_path | Bio.PriorityQueue |
| Text | Bio.Bam.Rec, Bio.Bam |
| throwErr | Bio.Iteratee, Bio.Bam |
| throwRecoverableErr | Bio.Iteratee, Bio.Bam |
| To | Bio.Genocall.Adna |
| toAvron | Data.Avro |
| toBin | Data.Avro |
| toException | Bio.Iteratee, Bio.Bam |
| toIterException | Bio.Iteratee, Bio.Bam |
| toList | Bio.Bam.Regions |
| toNucleotide | Bio.Base, Bio.TwoBit |
| toNucleotides | Bio.Base, Bio.TwoBit |
| toProb | Bio.Base, Bio.TwoBit |
| toQual | Bio.Base, Bio.TwoBit |
| toSchema | Data.Avro |
| trim_3 | Bio.Bam.Trim, Bio.Bam |
| trim_3' | Bio.Bam.Trim, Bio.Bam |
| trim_low_quality | Bio.Bam.Trim, Bio.Bam |
| tryHead | Bio.Iteratee, Bio.Bam |
| tryRun | Bio.Iteratee, Bio.Bam |
| TwoBitFile | Bio.TwoBit |
| type_mask | Bio.Bam.Rec, Bio.Bam |
| unaln_off | Bio.Bam.Index, Bio.Bam |
| Unexpected | Bio.Iteratee.ZLib |
| unfoldConvStream | Bio.Iteratee, Bio.Bam |
| unfoldConvStreamCheck | Bio.Iteratee, Bio.Bam |
| union | Bio.Bam.Pileup |
| univDamage | Bio.Genocall.Adna |
| Unknown | Bio.Bam.Header, Bio.Bam |
| unknownMapq | Bio.Bam.Header, Bio.Bam |
| unN | Bio.Base, Bio.TwoBit |
| unNs | Bio.Base, Bio.Bam.Rec, Bio.Bam, Bio.TwoBit |
| unpackBam | Bio.Bam.Rec, Bio.Bam |
| unpackSeqid | Bio.Base, Bio.TwoBit |
| unPr | Bio.Base, Bio.TwoBit |
| unQ | Bio.Base, Bio.TwoBit |
| unRefseq | Bio.Bam.Header, Bio.Bam |
| unsafePushByte | Bio.Iteratee.Builder |
| unsafePushByteString | Bio.Iteratee.Builder |
| unsafePushWord16 | Bio.Iteratee.Builder |
| unsafePushWord32 | Bio.Iteratee.Builder |
| unsafeSetMark | Bio.Iteratee.Builder |
| Unsorted | Bio.Bam.Header, Bio.Bam |
| updateE | Bio.Bam.Rec, Bio.Bam |
| upd_active | Bio.Bam.Pileup |
| upd_pos | Bio.Bam.Pileup |
| upd_waiting | Bio.Bam.Pileup |
| usedBytes | Bio.PriorityQueue |
| vec4 | Bio.Genocall.Adna |
| Vector_Nucs_half | Bio.Bam.Rec, Bio.Bam |
| VersionError | Bio.Iteratee.ZLib |
| viewMin | Bio.Bam.Pileup |
| virt_offset | Bio.Bam.Rec, Bio.Bam |
| V_Nuc | |
| 1 (Type/Class) | Bio.Bam.Pileup |
| 2 (Data Constructor) | Bio.Bam.Pileup |
| w2c | Bio.Base, Bio.TwoBit |
| wilson | Bio.Util |
| WindowBits | |
| 1 (Type/Class) | Bio.Iteratee.ZLib |
| 2 (Data Constructor) | Bio.Iteratee.ZLib |
| withFileFd | Bio.Iteratee, Bio.Bam |
| withPQ | Bio.PriorityQueue |
| Word32 | Bio.Bam.Rec, Bio.Bam |
| Word8 | Bio.Base, Bio.TwoBit |
| wordToDouble | Data.Avro |
| wordToFloat | Data.Avro |
| wrapIterExc | Bio.Iteratee, Bio.Bam |
| wrapRange | Bio.Base, Bio.TwoBit |
| wrapTo | Bio.Bam.Rmdup |
| writeAvroContainer | Data.Avro |
| writeBamFile | Bio.Bam.Writer, Bio.Bam |
| writeBamHandle | Bio.Bam.Writer, Bio.Bam |
| yield | Bio.Bam.Pileup |
| zag | Data.Avro |
| zagInt | Data.Avro |
| zig | Data.Avro |
| zigInt | Data.Avro |
| zipStreams | Bio.Iteratee, Bio.Bam |
| Zlib | Bio.Iteratee.ZLib |
| ZLibException | Bio.Iteratee.ZLib |
| ZLibParamsException | Bio.Iteratee.ZLib |
| _pb_chunks | Bio.Bam.Pileup |
| _pb_likes | Bio.Bam.Pileup |
| _pb_mapq | Bio.Bam.Pileup |
| _pb_rev | Bio.Bam.Pileup |
| _pb_wait | Bio.Bam.Pileup |