biohazard-0.6.5: bioinformatics support library

Index

!Bio.Genocall.Adna
$=Bio.Iteratee, Bio.Bam
$==Bio.Iteratee, Bio.Bam
:*Bio.Bam.Rec, Bio.Bam
:->Bio.Genocall.Adna
<#>Bio.Util.Numeric
<=<Bio.Iteratee, Bio.Bam
<>Bio.Base, Bio.TwoBit
<><Bio.Iteratee, Bio.Bam
=$Bio.Iteratee, Bio.Bam
><>Bio.Iteratee, Bio.Bam
>=>Bio.Iteratee, Bio.Bam
>>>Bio.Iteratee, Bio.Bam
AbsoluteEpsilonBio.Util.AD
ADBio.Util.AD
AD2Bio.Util.AD2
addBio.Bam.Regions
addIntBio.Bam.Regions
addPGBio.Bam.Header, Bio.Bam
add_activeBio.Bam.Pileup
adjustEBio.Bam.Rec, Bio.Bam
alignedLengthBio.Bam.Rec, Bio.Bam
All 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
Alt 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
AlternativeStopRuleBio.Util.AD
Any 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
appEndoBio.Base, Bio.TwoBit
ApproximateWolfeBio.Util.AD
AutoSwitchBio.Util.AD
AvroData.Avro
AvroMetaData.Avro
BamEnumerateeBio.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
BamOtherShitBio.Bam.Header, Bio.Bam
BamRawBio.Bam.Rec, Bio.Bam
bamRawBio.Bam.Rec, Bio.Bam
BamrawEnumerateeBio.Bam.Reader, Bio.Bam
BamRec 
1 (Type/Class)Bio.Bam.Rec, Bio.Bam
2 (Data Constructor)Bio.Bam.Rec, Bio.Bam
BamSortingBio.Bam.Header, Bio.Bam
BamSQ 
1 (Type/Class)Bio.Bam.Header, Bio.Bam
2 (Data Constructor)Bio.Bam.Header, Bio.Bam
BaseBio.Bam.Pileup
BasePileBio.Bam.Pileup
BB 
1 (Type/Class)Bio.Iteratee.Builder
2 (Data Constructor)Bio.Iteratee.Builder
BestCompressionBio.Iteratee.ZLib
BestSpeedBio.Iteratee.ZLib
BgzfChunkBio.Iteratee.Bgzf
bgzfEofMarkerBio.Iteratee.Bgzf
BinBio.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_contentsBio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam
block_offsetBio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam
BothBio.TwoBit
breakEBio.Iteratee, Bio.Bam
bufferBio.Iteratee.Builder
BufferErrorBio.Iteratee.ZLib
bumpBio.Bam.Pileup
b_cigarBio.Bam.Rec, Bio.Bam
b_extsBio.Bam.Rec, Bio.Bam
b_flagBio.Bam.Rec, Bio.Bam
b_isizeBio.Bam.Rec, Bio.Bam
b_mapqBio.Bam.Rec, Bio.Bam
b_mposBio.Bam.Rec, Bio.Bam
b_mrnmBio.Bam.Rec, Bio.Bam
b_posBio.Bam.Rec, Bio.Bam
b_qnameBio.Bam.Rec, Bio.Bam
b_qualBio.Bam.Rec, Bio.Bam
b_rnameBio.Bam.Rec, Bio.Bam
b_seqBio.Bam.Rec, Bio.Bam
b_virtual_offsetBio.Bam.Rec, Bio.Bam
CBio.Util.AD
C2Bio.Util.AD2
c2wBio.Base, Bio.TwoBit
called_sitesBio.Genocall.AvroFile
CallsBio.Genocall
CallStats 
1 (Type/Class)Bio.Bam.Pileup
2 (Data Constructor)Bio.Bam.Pileup
cancelAllBio.Iteratee, Bio.Bam
castData.Avro
CharBio.Bam.Rec, Bio.Bam
cheap_collapseBio.Bam.Rmdup
cheap_collapse_keepBio.Bam.Rmdup
checkErrBio.Iteratee, Bio.Bam
check_sortBio.Bam.Rmdup
chooseBio.Util.Numeric
ChunkBio.Iteratee, Bio.Bam
CigarBio.Bam.Rec, Bio.Bam
CigOpBio.Bam.Rec, Bio.Bam
clampPositionBio.TwoBit
clr_activeBio.Bam.Pileup
CollapseBio.Bam.Rmdup
combineCoordinatesBio.Bam.Reader, Bio.Bam
CombinedBio.Util.AD
combineNamesBio.Bam.Reader, Bio.Bam
compact_likelihoodsBio.Genocall.AvroFile
compareNamesBio.Bam.Header, Bio.Bam
complBio.Base, Bio.TwoBit
complexEntropyBio.Bam.Filter, Bio.Bam
complexSimpleBio.Bam.Filter, Bio.Bam
complsBio.Base, Bio.TwoBit
compressBgzfBio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam
compressBgzf'Bio.Iteratee.Bgzf
compressBgzfLvBio.Iteratee.Bgzf
compressBufferSizeBio.Iteratee.ZLib
compressChunkBio.Iteratee.Bgzf
compressDictionaryBio.Iteratee.ZLib
CompressionLevel 
1 (Type/Class)Bio.Iteratee.ZLib
2 (Data Constructor)Bio.Iteratee.ZLib
CompressionStrategyBio.Iteratee.ZLib
compression_levelBio.Iteratee.Bgzf
compressLevelBio.Iteratee.ZLib
compressMemoryLevelBio.Iteratee.ZLib
compressMethodBio.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
compressStrategyBio.Iteratee.ZLib
compressWindowBitsBio.Iteratee.ZLib
concatDefaultInputsBio.Bam.Reader, Bio.Bam
concatInputsBio.Bam.Reader, Bio.Bam
concatMapStreamBio.Iteratee, Bio.Bam
concatMapStreamMBio.Iteratee, Bio.Bam
conf_regionBio.Genocall.Metadata
consume_activeBio.Bam.Pileup
cons_collapseBio.Bam.Rmdup
cons_collapse_keepBio.Bam.Rmdup
ContainerOpts 
1 (Type/Class)Data.Avro
2 (Data Constructor)Data.Avro
convStreamBio.Iteratee, Bio.Bam
CoordinateBio.Bam.Header, Bio.Bam
DBio.Util.AD
D2Bio.Util.AD2
DamagedBaseBio.Bam.Pileup
DamageModelBio.Genocall.Adna
DamageParametersBio.Genocall.Adna
DataErrorBio.Iteratee.ZLib
DataRemainingBio.Iteratee, Bio.Bam
DBBio.Bam.Pileup
db_callBio.Bam.Pileup
db_dmgBio.Bam.Pileup
db_qualBio.Bam.Pileup
db_refBio.Bam.Pileup
debugParametersBio.Util.AD
DebugTolBio.Util.AD
debugTolBio.Util.AD
decodeAnyBamBio.Bam.Reader, Bio.Bam
decodeAnyBamFileBio.Bam.Reader, Bio.Bam
decodeAnyBamOrSamBio.Bam.Reader, Bio.Bam
decodeAnyBamOrSamFileBio.Bam.Reader, Bio.Bam
decodeBamBio.Bam.Reader, Bio.Bam
decodeIntBase128Data.Avro
decodeSamBio.Bam.Reader, Bio.Bam
decodeSam'Bio.Bam.Reader, Bio.Bam
decodeWordBase128Data.Avro
decomposeBio.Bam.Pileup
decompressBgzfBio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam
decompressBgzfBlocksBio.Iteratee.Bgzf, Bio.Bam.Reader, Bio.Bam
decompressBgzfBlocks'Bio.Iteratee.Bgzf
decompressBufferSizeBio.Iteratee.ZLib
decompressDictionaryBio.Iteratee.ZLib
DecompressParams 
1 (Type/Class)Bio.Iteratee.ZLib
2 (Data Constructor)Bio.Iteratee.ZLib
decompressPlainBio.Iteratee.Bgzf
decompressWindowBitsBio.Iteratee.ZLib
defaultBufSizeBio.Iteratee, Bio.Bam
DefaultCompressionBio.Iteratee.ZLib
defaultCompressParamsBio.Iteratee.ZLib
defaultDecompressParamsBio.Iteratee.ZLib
DefaultMemoryLevelBio.Iteratee.ZLib
defaultParametersBio.Util.AD
DefaultStopRuleBio.Util.AD
DefaultStrategyBio.Iteratee.ZLib
DefaultWindowBitsBio.Iteratee.ZLib
DeflatedBio.Iteratee.ZLib
DelBio.Bam.Rec, Bio.Bam
deleted_basesBio.Bam.Pileup
deleteEBio.Bam.Rec, Bio.Bam
deletePQBio.PriorityQueue
depthBio.Bam.Index, Bio.Bam
dequeuePQBio.PriorityQueue
deriveAvroData.Avro
deriveAvrosData.Avro
displayExceptionBio.Iteratee, Bio.Bam
distinctBinBio.Bam.Header, Bio.Bam
DivergentException 
1 (Data Constructor)Bio.Iteratee, Bio.Bam
2 (Type/Class)Bio.Iteratee, Bio.Bam
DivEst 
1 (Type/Class)Bio.Genocall.Metadata
2 (Data Constructor)Bio.Genocall.Metadata
doubleToWordData.Avro
DPBio.Genocall.Adna
dropStreamBio.Iteratee, Bio.Bam
dsd_deltaBio.Genocall.Adna
dsd_lambdaBio.Genocall.Adna
dsd_sigmaBio.Genocall.Adna
Dual 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
eflagMergedBio.Bam.Header, Bio.Bam
eflagTrimmedBio.Bam.Header, Bio.Bam
EmptyBio.Bam.Pileup
emptyBio.Iteratee, Bio.Bam
emptyQBio.Iteratee, Bio.Bam
encodeBamWithBio.Bam.Writer, Bio.Bam
encodeBgzfWithBio.Iteratee.Builder
encodeIntBase128Data.Avro
encodeWordBase128Data.Avro
endBio.Bam.Regions, Bio.Bam.Index, Bio.Bam
EndianBio.Iteratee, Bio.Bam
endianRead2Bio.Iteratee, Bio.Bam
endianRead3Bio.Iteratee, Bio.Bam
endianRead3iBio.Iteratee, Bio.Bam
endianRead4Bio.Iteratee, Bio.Bam
endianRead8Bio.Iteratee, Bio.Bam
Endo 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
EndOfReadBio.Bam.Pileup
endRecordBio.Iteratee.Builder
endRecordPart1Bio.Iteratee.Builder
endRecordPart2Bio.Iteratee.Builder
eneeBamRefseqBio.Bam.Index, Bio.Bam
eneeBamRegionsBio.Bam.Index, Bio.Bam
eneeBamSubseqBio.Bam.Index, Bio.Bam
eneeBamUnalignedBio.Bam.Index, Bio.Bam
eneeCheckIfDoneBio.Iteratee, Bio.Bam
eneeCheckIfDoneHandleBio.Iteratee, Bio.Bam
eneeCheckIfDoneIgnoreBio.Iteratee, Bio.Bam
eneeCheckIfDonePassBio.Iteratee, Bio.Bam
enqueuePQBio.PriorityQueue
enStrExcBio.Iteratee, Bio.Bam
ensureBufferBio.Iteratee.Builder
enumAuxFileBio.Iteratee, Bio.Bam
enumBlockFlushBio.Iteratee.ZLib
enumCheckIfDoneBio.Iteratee, Bio.Bam
enumChunkBio.Iteratee, Bio.Bam
enumDefaultInputsBio.Iteratee, Bio.Bam
enumDeflateBio.Iteratee.ZLib
enumEofBio.Iteratee, Bio.Bam
EnumerateeBio.Iteratee, Bio.Bam
Enumeratee'Bio.Iteratee, Bio.Bam
EnumerateeHandlerBio.Iteratee, Bio.Bam
EnumeratorBio.Iteratee, Bio.Bam
Enumerator'Bio.Iteratee, Bio.Bam
enumErrBio.Iteratee, Bio.Bam
EnumException 
1 (Data Constructor)Bio.Iteratee, Bio.Bam
2 (Type/Class)Bio.Iteratee, Bio.Bam
enumFdBio.Iteratee, Bio.Bam
enumFdRandomBio.Iteratee, Bio.Bam
enumFileBio.Iteratee, Bio.Bam
enumFileRandomBio.Iteratee, Bio.Bam
enumFromCallbackBio.Iteratee, Bio.Bam
enumFromCallbackCatchBio.Iteratee, Bio.Bam
enumFullFlushBio.Iteratee.ZLib
enumHandleBio.Iteratee, Bio.Bam
enumHandleRandomBio.Iteratee, Bio.Bam
enumInflateBio.Iteratee.ZLib
enumInflateAnyBio.Iteratee.ZLib
enumInputsBio.Iteratee, Bio.Bam
enumLinesBio.Iteratee, Bio.Bam
enumLinesBSBio.Iteratee, Bio.Bam
enumListBio.Iteratee, Bio.Bam
enumPure1ChunkBio.Iteratee, Bio.Bam
EnumStringException 
1 (Data Constructor)Bio.Iteratee, Bio.Bam
2 (Type/Class)Bio.Iteratee, Bio.Bam
enumSyncFlushBio.Iteratee.ZLib
EnumUnhandledIterException 
1 (Data Constructor)Bio.Iteratee, Bio.Bam
2 (Type/Class)Bio.Iteratee, Bio.Bam
enumWordsBio.Iteratee, Bio.Bam
enumWordsBSBio.Iteratee, Bio.Bam
EOFBio.Iteratee, Bio.Bam
EofErrorBio.Iteratee, Bio.Bam
EofException 
1 (Data Constructor)Bio.Iteratee, Bio.Bam
2 (Type/Class)Bio.Iteratee, Bio.Bam
EofNoErrorBio.Iteratee, Bio.Bam
EqualBio.Iteratee, Bio.Bam
errorContextsBio.Iteratee, Bio.Bam
errorMessageBio.Iteratee, Bio.Bam
estimateComplexityBio.Util.Numeric
EstimateErrorBio.Util.AD
estimateErrorBio.Util.AD
ExceptionBio.Iteratee, Bio.Bam
expandBufferBio.Iteratee.Builder
expm1Bio.Util.Numeric
ExtBio.Bam.Rec, Bio.Bam
extAsIntBio.Bam.Rec, Bio.Bam
extAsStringBio.Bam.Rec, Bio.Bam
extendRangeBio.Base, Bio.TwoBit
ExtensionsBio.Bam.Rec, Bio.Bam
extensionsBio.Bam.Index, Bio.Bam
FdBio.Iteratee, Bio.Bam
fileDriverBio.Iteratee, Bio.Bam
fileDriverRandomBio.Iteratee, Bio.Bam
fileDriverRandomVBufBio.Iteratee, Bio.Bam
fileDriverVBufBio.Iteratee, Bio.Bam
FileOffsetBio.Iteratee, Bio.Bam
filetype_labelData.Avro
FilteredBio.Iteratee.ZLib
filterPairsBio.Bam.Filter, Bio.Bam
filterStreamBio.Iteratee, Bio.Bam
filterStreamMBio.Iteratee, Bio.Bam
finalValueBio.Util.AD
findAuxFileBio.Base, Bio.TwoBit
findSchemaData.Avro
First 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
fixupBwaFlagsBio.Bam.Evan
fixupFlagAbuseBio.Bam.Evan
flagAuxillaryBio.Bam.Header, Bio.Bam
flagDuplicateBio.Bam.Header, Bio.Bam
flagFailsQCBio.Bam.Header, Bio.Bam
flagFirstMateBio.Bam.Header, Bio.Bam
flagMateReversedBio.Bam.Header, Bio.Bam
flagMateUnmappedBio.Bam.Header, Bio.Bam
flagPairedBio.Bam.Header, Bio.Bam
flagProperlyPairedBio.Bam.Header, Bio.Bam
flagReversedBio.Bam.Header, Bio.Bam
flagSecondMateBio.Bam.Header, Bio.Bam
flagUnmappedBio.Bam.Header, Bio.Bam
FloatBio.Bam.Rec, Bio.Bam
float2miniData.MiniFloat
FloatArrBio.Bam.Rec, Bio.Bam
floatToWordData.Avro
foldChunksMBio.Iteratee, Bio.Bam
foldStreamBio.Iteratee, Bio.Bam
foldStreamMBio.Iteratee, Bio.Bam
FormatBio.Iteratee.ZLib
fromBinData.Avro
fromExceptionBio.Iteratee, Bio.Bam
fromIterExceptionBio.Iteratee, Bio.Bam
fromListBio.Bam.Regions
fromProbBio.Base, Bio.TwoBit
fromQualBio.Base, Bio.TwoBit
fromQualRaisedBio.Base, Bio.TwoBit
funcEpsilonBio.Util.AD
funcEvalsBio.Util.AD
FunctionBio.Util.AD
FunctionChangeBio.Util.AD
FunctionValueNaNBio.Util.AD
gapBio.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
genSubstMatBio.Genocall.Adna
getAllBio.Base, Bio.TwoBit
getAltBio.Base, Bio.TwoBit
getAnyBio.Base, Bio.TwoBit
getBamRawBio.Bam.Reader, Bio.Bam
getChunkBio.Iteratee, Bio.Bam
getChunksBio.Iteratee, Bio.Bam
getDualBio.Base, Bio.TwoBit
getFirstBio.Base, Bio.TwoBit
getFwdSubseqWithBio.TwoBit
getLastBio.Base, Bio.TwoBit
getLazySubseqBio.TwoBit
getMdBio.Bam.Rec, Bio.Bam
getMinKeyBio.Bam.Pileup
getMinPQBio.PriorityQueue
getNamedSchemaData.Avro
getOffsetBio.Iteratee.Bgzf
getProductBio.Base, Bio.TwoBit
getRandomSeqBio.TwoBit
getRefBio.Bam.Header, Bio.Bam
getRefseqsBio.Genocall.AvroFile
getSeqLengthBio.TwoBit
getSeqnamesBio.TwoBit
getSubseqBio.TwoBit
getSubseqAsciiBio.TwoBit
getSubseqMaskedBio.TwoBit
getSubseqWithBio.TwoBit
getSumBio.Base, Bio.TwoBit
get_activeBio.Bam.Pileup
get_posBio.Bam.Pileup
get_refseqBio.Bam.Pileup
get_waitingBio.Bam.Pileup
GLBio.Bam.Pileup
GloballyBio.Align
gradEvalsBio.Util.AD
GradientBio.Util.AD
GradientMVectorBio.Util.AD
gradNormBio.Util.AD
GroupedBio.Bam.Header, Bio.Bam
GroupSortedBio.Bam.Header, Bio.Bam
groupStreamByBio.Iteratee, Bio.Bam
groupStreamOnBio.Iteratee, Bio.Bam
GZipBio.Iteratee.ZLib
GZipOrZlibBio.Iteratee.ZLib
HardBio.TwoBit
HasPrefixBio.Align
hdr_other_shitBio.Bam.Header, Bio.Bam
hdr_sortingBio.Bam.Header, Bio.Bam
hdr_versionBio.Bam.Header, Bio.Bam
headsBio.Iteratee, Bio.Bam
headStreamBio.Iteratee, Bio.Bam
HeapBio.Bam.Pileup
HMaBio.Bam.Rec, Bio.Bam
HuffmanOnlyBio.Iteratee.ZLib
icontBio.Iteratee, Bio.Bam
icontMBio.Iteratee, Bio.Bam
idoneBio.Iteratee, Bio.Bam
idoneMBio.Iteratee, Bio.Bam
IExceptionBio.Iteratee, Bio.Bam
IFException 
1 (Data Constructor)Bio.Iteratee, Bio.Bam
2 (Type/Class)Bio.Iteratee, Bio.Bam
ifoldBio.Iteratee, Bio.Bam
iGetStringBio.Iteratee, Bio.Bam
iliftBio.Iteratee, Bio.Bam
iLookAheadBio.Iteratee, Bio.Bam
IncorrectCompressionLevelBio.Iteratee.ZLib
IncorrectMemoryLevelBio.Iteratee.ZLib
IncorrectStateBio.Iteratee.ZLib
IncorrectWindowBitsBio.Iteratee.ZLib
IndelBio.Bam.Pileup
IndelPileBio.Bam.Pileup
IndelVariant 
1 (Type/Class)Bio.Bam.Pileup
2 (Data Constructor)Bio.Bam.Pileup
indel_likelihoodsBio.Genocall.AvroFile
indel_statsBio.Genocall.AvroFile
indel_variantsBio.Genocall.AvroFile
initialStepBio.Util.AD
initial_schemasData.Avro
InsBio.Bam.Rec, Bio.Bam
insertEBio.Bam.Rec, Bio.Bam
inserted_basesBio.Bam.Pileup
insideRangeBio.Base, Bio.TwoBit
ins_waitingBio.Bam.Pileup
IntBio.Bam.Rec, Bio.Bam
IntArrBio.Bam.Rec, Bio.Bam
invalidPosBio.Bam.Header, Bio.Bam
invalidRefseqBio.Bam.Header, Bio.Bam
invnormcdfBio.Util.Numeric
ioBindBio.Iteratee, Bio.Bam
ioBind_Bio.Iteratee, Bio.Bam
isAuxillaryBio.Bam.Rec, Bio.Bam
isBamBio.Bam.Reader, Bio.Bam
isBamOrSamBio.Bam.Reader, Bio.Bam
IsBamRecBio.Bam.Writer, Bio.Bam
isBaseBio.Base, Bio.TwoBit
isBgzfBio.Iteratee.Bgzf
isBgzfBamBio.Bam.Reader, Bio.Bam
isDuplicateBio.Bam.Rec, Bio.Bam
isFailsQCBio.Bam.Rec, Bio.Bam
isFinishedBio.Iteratee, Bio.Bam
isFirstMateBio.Bam.Rec, Bio.Bam
isGapBio.Base, Bio.TwoBit
isGzipBio.Iteratee.Bgzf
isGzipBamBio.Bam.Reader, Bio.Bam
isigmoid2Bio.Util.Numeric
isKnownMapqBio.Bam.Header, Bio.Bam
isMateReversedBio.Bam.Rec, Bio.Bam
isMateUnmappedBio.Bam.Rec, Bio.Bam
isMergedBio.Bam.Rec, Bio.Bam
isPairedBio.Bam.Rec, Bio.Bam
isPlainBamBio.Bam.Reader, Bio.Bam
IsPrefixBio.Align
isProperBaseBio.Base, Bio.TwoBit
isProperlyPairedBio.Bam.Rec, Bio.Bam
isReversedBio.Bam.Rec, Bio.Bam
isSecondMateBio.Bam.Rec, Bio.Bam
isStreamFinishedBio.Iteratee, Bio.Bam
isTrimmedBio.Bam.Rec, Bio.Bam
isUnmappedBio.Bam.Rec, Bio.Bam
isValidPosBio.Bam.Header, Bio.Bam
isValidRefseqBio.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
iterExceptionFromExceptionBio.Iteratee, Bio.Bam
iterExceptionToExceptionBio.Iteratee, Bio.Bam
iterGetBio.Iteratee, Bio.Bam
iterLoopBio.Iteratee, Bio.Bam
iterStrExcBio.Iteratee, Bio.Bam
IterStringException 
1 (Data Constructor)Bio.Iteratee, Bio.Bam
2 (Type/Class)Bio.Iteratee, Bio.Bam
joinIBio.Iteratee, Bio.Bam
joinIMBio.Iteratee, Bio.Bam
Last 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
LeftoverChunkBio.Iteratee.Bgzf
lenBio.Iteratee.Builder
lengthQBio.Iteratee, Bio.Bam
LessBio.Iteratee, Bio.Bam
Library 
1 (Type/Class)Bio.Genocall.Metadata
2 (Data Constructor)Bio.Genocall.Metadata
library_damageBio.Genocall.Metadata
library_filesBio.Genocall.Metadata
library_nameBio.Genocall.Metadata
liftBio.Iteratee, Bio.Bam
liftBlockBio.Iteratee.Bgzf
liftIBio.Iteratee, Bio.Bam
liftIOBio.Iteratee, Bio.Bam
LineSearchBio.Util.AD
lineSearchBio.Util.AD
LineSearchFailsBisectionBio.Util.AD
LineSearchFailsInitialBio.Util.AD
LineSearchFailsUpdateBio.Util.AD
ListLikeBio.Iteratee, Bio.Bam
llerpBio.Util.Numeric
lMapBio.Iteratee, Bio.Bam
log1pBio.Util.Numeric
lookupLTBio.Bam.Regions
lookupSequenceBio.TwoBit
LooseMapBio.Iteratee, Bio.Bam
LSBBio.Iteratee, Bio.Bam
lsumBio.Util.Numeric
makePQBio.PriorityQueue
mapChunksBio.Iteratee, Bio.Bam
mapChunksMBio.Iteratee, Bio.Bam
mapChunksM_Bio.Iteratee, Bio.Bam
mapIterateeBio.Iteratee, Bio.Bam
mapMaybeStreamBio.Iteratee, Bio.Bam
mappendBio.Base, Bio.TwoBit
mapStreamBio.Iteratee, Bio.Bam
mapStreamMBio.Iteratee, Bio.Bam
mapStreamM_Bio.Iteratee, Bio.Bam
maq_snp_callBio.Genocall
markBio.Iteratee.Builder
mark2Bio.Iteratee.Builder
MaskBio.TwoBit
MatBio.Bam.Rec, Bio.Bam
maxBlockSizeBio.Iteratee.Bgzf
maxItersFacBio.Util.AD
MaxMemoryLevelBio.Iteratee.ZLib
MaxSecantIterBio.Util.AD
MaxTotalIterBio.Util.AD
max_mbBio.PriorityQueue
mBindBio.Iteratee, Bio.Bam
mBind_Bio.Iteratee, Bio.Bam
MCombinedBio.Util.AD
mconcatBio.Base, Bio.TwoBit
MdDelBio.Bam.Header, Bio.Bam
MdNumBio.Bam.Header, Bio.Bam
MdOpBio.Bam.Header, Bio.Bam
MdRepBio.Bam.Header, Bio.Bam
memoDamageModelBio.Genocall.Adna
memoObjectData.Avro
MemoryErrorBio.Iteratee.ZLib
MemoryLevel 
1 (Type/Class)Bio.Iteratee.ZLib
2 (Data Constructor)Bio.Iteratee.ZLib
memptyBio.Base, Bio.TwoBit
mergeBlocksBio.TwoBit
mergeDefaultInputsBio.Bam.Reader, Bio.Bam
mergeEnumsBio.Iteratee, Bio.Bam
mergeEnums'Bio.Iteratee, Bio.Bam
mergeInputsBio.Bam.Reader, Bio.Bam
mergeSortStreamsBio.Iteratee, Bio.Bam
MetadataBio.Genocall.Metadata
meta_commentBio.Bam.Header, Bio.Bam
meta_hdrBio.Bam.Header, Bio.Bam
meta_infoData.Avro
meta_other_shitBio.Bam.Header, Bio.Bam
meta_refsBio.Bam.Header, Bio.Bam
MethodBio.Iteratee.ZLib
MFunctionBio.Util.AD
MGradientBio.Util.AD
Mini 
1 (Type/Class)Data.MiniFloat
2 (Data Constructor)Data.MiniFloat
mini2floatData.MiniFloat
minimizeBio.Util.AD
MinMemoryLevelBio.Iteratee.ZLib
minshiftBio.Bam.Index, Bio.Bam
MkSchema 
1 (Type/Class)Data.Avro
2 (Data Constructor)Data.Avro
mkSchemaData.Avro
mk_snp_gtsBio.Genocall
ModeBio.Align
MonadIOBio.Iteratee, Bio.Bam
MonadMaskBio.Iteratee, Bio.Bam
MonoidBio.Base, Bio.TwoBit
MSBBio.Iteratee, Bio.Bam
MutableBio.Util.AD
myersAlignBio.Align
NBio.Base, Bio.TwoBit
nanRhoBio.Util.AD
NeedDictionaryBio.Iteratee.ZLib
NegativeSlopeBio.Util.AD
newBufferBio.Iteratee.Builder
nexpandBio.Util.AD
NoChunkBio.Iteratee.Bgzf
NoCompressionBio.Iteratee.ZLib
noDamageBio.Genocall.Adna
NodeBio.Bam.Pileup
NoneBio.TwoBit
NopBio.Bam.Rec, Bio.Bam
noRefsBio.Bam.Header, Bio.Bam
normalizeToBio.Bam.Rmdup
NotDescentBio.Util.AD
NotLessBio.Iteratee, Bio.Bam
NsBio.Base, Bio.Bam.Rec, Bio.Bam, Bio.TwoBit
nsecantBio.Util.AD
nucABio.Base, Bio.TwoBit
nucCBio.Base, Bio.TwoBit
nucGBio.Base, Bio.TwoBit
NucleotideBio.Base, Bio.TwoBit
NucleotidesBio.Base, Bio.Bam.Rec, Bio.Bam, Bio.TwoBit
nucsABio.Base, Bio.TwoBit
nucsCBio.Base, Bio.TwoBit
nucsGBio.Base, Bio.TwoBit
nucsNBio.Base, Bio.TwoBit
nucsTBio.Base, Bio.TwoBit
nucTBio.Base, Bio.TwoBit
nucToNucsBio.Base, Bio.TwoBit
NullableBio.Iteratee, Bio.Bam
nullBamRecBio.Bam.Rec, Bio.Bam
nullCBio.Iteratee, Bio.Bam
NullPointBio.Iteratee, Bio.Bam
objects_per_blockData.Avro
openTwoBitBio.TwoBit
optimizeBio.Util.AD
Ordering'Bio.Iteratee, Bio.Bam
overlapsBio.Bam.Regions
p'check_waitingBio.Bam.Pileup
p'feed_inputBio.Bam.Pileup
p'scan_activeBio.Bam.Pileup
packSeqidBio.Base, Bio.TwoBit
PadBio.Bam.Rec, Bio.Bam
Parameters 
1 (Data Constructor)Bio.Util.AD
2 (Type/Class)Bio.Util.AD
paramVectorBio.Util.AD
paramVector2Bio.Util.AD2
parMapChunksIOBio.Iteratee, Bio.Iteratee.Bgzf, Bio.Bam
parseBamMetaBio.Bam.Header, Bio.Bam
parseBamMetaLineBio.Bam.Header, Bio.Bam
ParseError 
1 (Type/Class)Bio.Iteratee, Bio.Bam
2 (Data Constructor)Bio.Iteratee, Bio.Bam
parseFastqBio.Bam.Fastq, Bio.Bam
parseFastq'Bio.Bam.Fastq, Bio.Bam
parseFastqCassavaBio.Bam.Fastq, Bio.Bam
parserToIterateeBio.Iteratee, Bio.Bam
partitionPairEithersBio.Bam.Pileup
peekBio.Bam.Pileup
peekMinPQBio.PriorityQueue
peekStreamBio.Iteratee, Bio.Bam
Pile 
1 (Type/Class)Bio.Bam.Pileup
2 (Data Constructor)Bio.Bam.Pileup
Pile'Bio.Bam.Pileup
PileFBio.Bam.Pileup
PileM 
1 (Type/Class)Bio.Bam.Pileup
2 (Data Constructor)Bio.Bam.Pileup
pileupBio.Bam.Pileup
pileup'Bio.Bam.Pileup
pileup''Bio.Bam.Pileup
pipeBamOutputBio.Bam.Writer, Bio.Bam
pipeSamOutputBio.Bam.Writer, Bio.Bam
PointMVectorBio.Util.AD
point_estBio.Genocall.Metadata
popQBio.Iteratee, Bio.Bam
PosBio.Base, Bio.TwoBit
PositionBio.Base, Bio.TwoBit
PosPrimChunksBio.Bam.Pileup
powBio.Base, Bio.TwoBit
PQBio.PriorityQueue
PQ_Conf 
1 (Type/Class)Bio.PriorityQueue
2 (Data Constructor)Bio.PriorityQueue
PrBio.Base, Bio.TwoBit
PrimBaseBio.Bam.Pileup
PrimChunksBio.Bam.Pileup
printFinalBio.Util.AD
printLinesBio.Iteratee, Bio.Bam
printLinesUnterminatedBio.Iteratee, Bio.Bam
printParamsBio.Util.AD
ProbBio.Base, Bio.TwoBit
Prob'Bio.Base, Bio.TwoBit
probToQualBio.Base, Bio.TwoBit
Product 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
progressBamBio.Bam.Rec, Bio.Bam
progressNumBio.Iteratee, Bio.Bam
progressPosBio.Iteratee, Bio.Bam
properBasesBio.Base, Bio.TwoBit
protectTermBio.Iteratee, Bio.Bam
Push 
1 (Type/Class)Bio.Iteratee.Builder
2 (Data Constructor)Bio.Iteratee.Builder
pushBamBio.Bam.Writer, Bio.Bam
pushBuilderBio.Iteratee.Builder
pushByteBio.Iteratee.Builder
pushByteStringBio.Iteratee.Builder
pushFloatBio.Iteratee.Builder
pushQBio.Iteratee, Bio.Bam
pushWord16Bio.Iteratee.Builder
pushWord32Bio.Iteratee.Builder
p_indel_pileBio.Bam.Pileup
p_indel_statBio.Bam.Pileup
p_is_reverseBio.Base, Bio.TwoBit
p_posBio.Bam.Pileup
p_refseqBio.Bam.Pileup
p_seqBio.Base, Bio.TwoBit
p_snp_pileBio.Bam.Pileup
p_snp_statBio.Bam.Pileup
p_startBio.Base, Bio.TwoBit
QBio.Base, Bio.TwoBit
qdecayBio.Util.AD
QQ 
1 (Type/Class)Bio.Iteratee, Bio.Bam
2 (Data Constructor)Bio.Iteratee, Bio.Bam
quadraticStepBio.Util.AD
QualBio.Base, Bio.TwoBit
QualFilterBio.Bam.Filter, Bio.Bam
qualityAverageBio.Bam.Filter, Bio.Bam
qualityFromNewIlluminaBio.Bam.Filter, Bio.Bam
qualityFromOldIlluminaBio.Bam.Filter, Bio.Bam
qualityMinimumBio.Bam.Filter, Bio.Bam
qualToProbBio.Base, Bio.TwoBit
QuerynameBio.Bam.Header, Bio.Bam
queue_depthBio.Iteratee.Bgzf
QuietBio.Util.AD
quietParametersBio.Util.AD
Range 
1 (Type/Class)Bio.Base, Bio.TwoBit
2 (Data Constructor)Bio.Base, Bio.TwoBit
RawBio.Iteratee.ZLib
raw_dataBio.Bam.Rec, Bio.Bam
readAvroContainerData.Avro
readBaiIndexBio.Bam.Index, Bio.Bam
readBamIndexBio.Bam.Index, Bio.Bam
readMdBio.Bam.Header, Bio.Bam
readMetadataBio.Genocall.Metadata
reads_mapq0Bio.Bam.Pileup
readTabixBio.Bam.Index, Bio.Bam
readWord16be_bsBio.Iteratee, Bio.Bam
readWord16le_bsBio.Iteratee, Bio.Bam
readWord32be_bsBio.Iteratee, Bio.Bam
readWord32le_bsBio.Iteratee, Bio.Bam
readWord64be_bsBio.Iteratee, Bio.Bam
readWord64le_bsBio.Iteratee, Bio.Bam
read_depthBio.Bam.Pileup
RecordChunkBio.Iteratee.Bgzf
reference_nameBio.Genocall.AvroFile
RefsBio.Bam.Header, Bio.Bam
Refseq 
1 (Type/Class)Bio.Bam.Header, Bio.Bam
2 (Data Constructor)Bio.Bam.Header, Bio.Bam
refseqBio.Bam.Regions, Bio.Bam.Index, Bio.Bam
refseq_binsBio.Bam.Index, Bio.Bam
refseq_ckpointsBio.Bam.Index, Bio.Bam
ref_alleleBio.Genocall.AvroFile
regCompBio.Util.Regex
RegexBio.Util.Regex
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
regMatchBio.Util.Regex
RelativeEpsilonBio.Util.AD
removeWartsBio.Bam.Evan
restartFacBio.Util.AD
ResultBio.Util.AD
reverseRangeBio.Base, Bio.TwoBit
rmdupBio.Bam.Rmdup
runBio.Iteratee, Bio.Bam
runIterBio.Iteratee, Bio.Bam
runMkSchemaData.Avro
runPileMBio.Bam.Pileup
r_lengthBio.Base, Bio.TwoBit
r_posBio.Base, Bio.TwoBit
Sample 
1 (Type/Class)Bio.Genocall.Metadata
2 (Data Constructor)Bio.Genocall.Metadata
sample_avro_filesBio.Genocall.Metadata
sample_bcf_filesBio.Genocall.Metadata
sample_divergencesBio.Genocall.Metadata
sample_div_tablesBio.Genocall.Metadata
sample_librariesBio.Genocall.Metadata
SeekBio.Bam.Pileup
seekBio.Iteratee, Bio.Bam
SeekException 
1 (Data Constructor)Bio.Iteratee, Bio.Bam
2 (Type/Class)Bio.Iteratee, Bio.Bam
SeqidBio.Base, Bio.TwoBit
setEOFBio.Iteratee, Bio.Bam
setMarkBio.Iteratee.Builder
setQualFlagBio.Bam.Rec, Bio.Bam
set_posBio.Bam.Pileup
set_waitingBio.Bam.Pileup
shiftPositionBio.Base, Bio.TwoBit
shiftRangeBio.Base, Bio.TwoBit
showAlignedBio.Align
showBamMetaBio.Bam.Header, Bio.Bam
showMdBio.Bam.Header, Bio.Bam
showNucleotideBio.Base, Bio.TwoBit
showNucleotidesBio.Base, Bio.TwoBit
showNumBio.Util.Numeric
showOOMBio.Util.Numeric
sigmoid2Bio.Util.Numeric
SimpleBio.Util.AD
simple_callBio.Genocall
simple_indel_callBio.Genocall
simple_snp_callBio.Genocall
SizeableBio.PriorityQueue
sizePQBio.PriorityQueue
skipToEofBio.Iteratee, Bio.Bam
SMaBio.Bam.Rec, Bio.Bam
Snp_GLs 
1 (Type/Class)Bio.Genocall
2 (Data Constructor)Bio.Genocall
snp_glsBio.Genocall
snp_likelihoodsBio.Genocall.AvroFile
snp_statsBio.Genocall.AvroFile
SoftBio.TwoBit
SpecialChunkBio.Iteratee.Bgzf
split_sam_rgnsBio.Genocall.Metadata
sq_lengthBio.Bam.Header, Bio.Bam
sq_nameBio.Bam.Header, Bio.Bam
sq_other_shitBio.Bam.Header, Bio.Bam
ssd_deltaBio.Genocall.Adna
ssd_kappaBio.Genocall.Adna
ssd_lambdaBio.Genocall.Adna
ssd_sigmaBio.Genocall.Adna
startBio.Bam.Regions, Bio.Bam.Index, Bio.Bam
StartFunctionValueNaNBio.Util.AD
start_positionBio.Genocall.AvroFile
Statistics 
1 (Data Constructor)Bio.Util.AD
2 (Type/Class)Bio.Util.AD
stderrBio.Iteratee, Bio.Bam
stdinBio.Iteratee, Bio.Bam
stdoutBio.Iteratee, Bio.Bam
StopRulesBio.Util.AD
stopRulesBio.Util.AD
StreamBio.Iteratee, Bio.Bam
stream2vectorBio.Iteratee, Bio.Bam
stream2vectorNBio.Iteratee, Bio.Bam
StreamErrorBio.Iteratee.ZLib
StreamStatusBio.Iteratee, Bio.Bam
subsampleBamBio.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 
1 (Data Constructor)Bio.Base, Bio.TwoBit
2 (Type/Class)Bio.Base, Bio.TwoBit
sum_mapqBio.Bam.Pileup
sum_mapq_squaredBio.Bam.Pileup
takeOverlapBio.TwoBit
takeStreamBio.Iteratee, Bio.Bam
takeWhileEBio.Iteratee, Bio.Bam
TBFBio.TwoBit
tbf_rawBio.TwoBit
tbf_seqsBio.TwoBit
TBSBio.TwoBit
tbs_dna_offsetBio.TwoBit
tbs_dna_sizeBio.TwoBit
tbs_m_blocksBio.TwoBit
tbs_n_blocksBio.TwoBit
techDeltaBio.Util.AD
techEtaBio.Util.AD
techGammaBio.Util.AD
TechParameters 
1 (Data Constructor)Bio.Util.AD
2 (Type/Class)Bio.Util.AD
techParametersBio.Util.AD
techPsi0Bio.Util.AD
techPsi1Bio.Util.AD
techPsi2Bio.Util.AD
techRhoBio.Util.AD
techSigmaBio.Util.AD
temp_pathBio.PriorityQueue
TextBio.Bam.Rec, Bio.Bam
throwErrBio.Iteratee, Bio.Bam
throwRecoverableErrBio.Iteratee, Bio.Bam
ToBio.Genocall.Adna
toAvronData.Avro
toBinData.Avro
toExceptionBio.Iteratee, Bio.Bam
toIterExceptionBio.Iteratee, Bio.Bam
ToleranceStatisfiedBio.Util.AD
toListBio.Bam.Regions
toNucleotideBio.Base, Bio.TwoBit
toNucleotidesBio.Base, Bio.TwoBit
toProbBio.Base, Bio.TwoBit
toQualBio.Base, Bio.TwoBit
toSchemaData.Avro
totalItersBio.Util.AD
trim_3Bio.Bam.Trim, Bio.Bam
trim_3'Bio.Bam.Trim, Bio.Bam
trim_low_qualityBio.Bam.Trim, Bio.Bam
tryHeadBio.Iteratee, Bio.Bam
tryRunBio.Iteratee, Bio.Bam
TwoBitFileBio.TwoBit
TwoBitSequenceBio.TwoBit
type_maskBio.Bam.Rec, Bio.Bam
unaln_offBio.Bam.Index, Bio.Bam
UnexpectedBio.Iteratee.ZLib
unfoldConvStreamBio.Iteratee, Bio.Bam
unfoldConvStreamCheckBio.Iteratee, Bio.Bam
unionBio.Bam.Pileup
univDamageBio.Genocall.Adna
UnknownBio.Bam.Header, Bio.Bam
unknownMapqBio.Bam.Header, Bio.Bam
unMiniData.MiniFloat
unNBio.Base, Bio.TwoBit
unNsBio.Base, Bio.Bam.Rec, Bio.Bam, Bio.TwoBit
unpackBamBio.Bam.Rec, Bio.Bam
unpackSeqidBio.Base, Bio.TwoBit
unPrBio.Base, Bio.TwoBit
unQBio.Base, Bio.TwoBit
unRefseqBio.Bam.Header, Bio.Bam
unsafePushByteBio.Iteratee.Builder
unsafePushByteStringBio.Iteratee.Builder
unsafePushFloatBio.Iteratee.Builder
unsafePushWord16Bio.Iteratee.Builder
unsafePushWord32Bio.Iteratee.Builder
unsafeSetMarkBio.Iteratee.Builder
UnsortedBio.Bam.Header, Bio.Bam
updateEBio.Bam.Rec, Bio.Bam
updateMetadataBio.Genocall.Metadata
upd_activeBio.Bam.Pileup
upd_posBio.Bam.Pileup
usedBytesBio.PriorityQueue
VCombinedBio.Util.AD
Vector_Nucs_halfBio.Bam.Rec, Bio.Bam
Verbose 
1 (Data Constructor)Bio.Util.AD
2 (Type/Class)Bio.Util.AD
verboseBio.Util.AD
VersionErrorBio.Iteratee.ZLib
VeryVerboseBio.Util.AD
VFunctionBio.Util.AD
VGradientBio.Util.AD
viewMinBio.Bam.Pileup
virt_offsetBio.Bam.Rec, Bio.Bam
V_Nuc 
1 (Type/Class)Bio.Bam.Pileup
2 (Data Constructor)Bio.Bam.Pileup
V_Nucs 
1 (Type/Class)Bio.Bam.Pileup
2 (Data Constructor)Bio.Bam.Pileup
w2cBio.Base, Bio.TwoBit
wilsonBio.Util.Numeric
WindowBits 
1 (Type/Class)Bio.Iteratee.ZLib
2 (Data Constructor)Bio.Iteratee.ZLib
withFileFdBio.Iteratee, Bio.Bam
withPQBio.PriorityQueue
Word32Bio.Bam.Rec, Bio.Bam
Word8Bio.Base, Bio.TwoBit
wordToDoubleData.Avro
wordToFloatData.Avro
wrapIterExcBio.Iteratee, Bio.Bam
wrapRangeBio.Base, Bio.TwoBit
wrapToBio.Bam.Rmdup
writeAvroContainerData.Avro
writeBamFileBio.Bam.Writer, Bio.Bam
writeBamHandleBio.Bam.Writer, Bio.Bam
yieldBio.Bam.Pileup
zagData.Avro
zagIntData.Avro
zigData.Avro
zigIntData.Avro
zipStreamsBio.Iteratee, Bio.Bam
ZlibBio.Iteratee.ZLib
ZLibExceptionBio.Iteratee.ZLib
ZLibParamsExceptionBio.Iteratee.ZLib
_pb_chunksBio.Bam.Pileup
_pb_likesBio.Bam.Pileup
_pb_mapqBio.Bam.Pileup
_pb_revBio.Bam.Pileup
_pb_waitBio.Bam.Pileup