Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

addLink() (in BM_linkPair)	aln() (in BamMaker)

B

bam_ID (in BM_linkInfo_C)	BamMException (in bamm.bammExceptions)	BM_coverageType_C (in bamm.cWrapper)
bamExtractor (in bamm)	bammExceptions (in bamm)	BM_fileInfo (in bamm.bamFile)
BamExtractor (in bamm.bamExtractor)	bamParser (in bamm)	BM_fileInfo_C (in bamm.cWrapper)
bamFile (in bamm)	BamParser (in bamm.bamParser)	BM_linkInfo (in bamm.bamLink)
BAMFileNotFoundException (in bamm.bammExceptions)	bamRead (in bamm)	BM_linkInfo_C (in bamm.cWrapper)
bamFiles (in BM_fileInfo_C)	BamScheduler (in bamm.bamMaker)	BM_linkPair (in bamm.bamLink)
BAMIndexNotFoundException (in bamm.bammExceptions)	BM_bamFile (in bamm.bamFile)	BM_linkPair_C (in bamm.cWrapper)
bamLink (in bamm)	BM_bamFile_C (in bamm.cWrapper)	BM_LinkWalker_C (in bamm.cWrapper)
bamm	BM_bamType (in bamm.bamFile)	BM_mappedRead_C (in bamm.cWrapper)
bamMaker (in bamm)	BM_bamType_C (in bamm.cWrapper)	bwasw() (in BamMaker)
BamMaker (in bamm.bamMaker)	BM_coverageType (in bamm.bamFile)	bwasw_to_sorted_indexed_bam() (in BamMaker)

C

C_MEAN (in CT)	consume() (in BM_fileInfo)	coverageType (in BM_fileInfo_C)
cfuhash_table_t (in bamm.cWrapper)	contigLengths (in BM_fileInfo_C)	CT (in bamm.cWrapper)
checkForDatabase() (in bamm.bamMaker)	contigNameLengths (in BM_fileInfo_C)	CT2Str() (in bamm.cWrapper)
cid1 (in BM_linkPair_C)	contigNames (in BM_fileInfo_C)	cWrapper (in bamm)
cid2 (in BM_linkPair_C)	COUNT (in CT)	CWrapper (in bamm.cWrapper)
collapseBFIs() (in BamParser)	coverages (in BM_fileInfo_C)

D

determineFileSuffix() (in ReadSet)

E

enum() (in bamm.cWrapper)	ERROR (in RPI)	extract() (in BamExtractor)
ER_EM_EG (in MI)	externalExtractWrapper() (in bamm.bamExtractor)
ERROR (in OT)	externalParseWrapper() (in bamm.bamParser)

F

fileName (in BM_bamFile_C)	FIR (in RPI)
fileNameLength (in BM_bamFile_C)	freeReadSet() (in ReadSetManager)

G

getConstFP() (in ReadSet)	getReadSet() (in ReadSetManager)	group (in BM_mappedRead_C)

I

K

keyCount (in BM_LinkWalker_C)	keys (in BM_LinkWalker_C)

L

LI (in BM_LinkWalker_C)	links (in BM_LinkWalker_C)	lowerCut (in BM_coverageType_C)
LI (in BM_linkPair_C)	links (in BM_fileInfo_C)

M

makeBam() (in BamMaker)	makeSurePathExists() (in BamExtractor)	mem_to_sorted_indexed_bam() (in BamMaker)
makeBams() (in BamScheduler)	makeSurePathExists() (in BamScheduler)	mi (in BM_mappedRead_C)
makeDatabase() (in BamMaker)	managePrintQueue() (in BamExtractor)	MI (in bamm.cWrapper)
makeKey() (in BM_linkPair)	manageRequests() (in ReadSetManager)	MI2Str() (in bamm.cWrapper)
makeOutFileName() (in BamScheduler)	mem_single_to_sorted_indexed_bam() (in BamMaker)	MixedFileTypesException (in bamm.bammExceptions)

N

nextLink (in BM_linkInfo_C)	NONE (in CT)	numKeys (in BM_LinkWalker_C)
nextPrintingRead (in BM_mappedRead_C)	NONE (in OT)	numLinks (in BM_linkPair_C)
nextRead (in BM_mappedRead_C)	numBams (in BM_fileInfo_C)	numTypes (in BM_bamFile_C)
NoBAMSFoundException (in bamm.bammExceptions)	numContigs (in BM_fileInfo_C)

O

organiseOutFiles() (in ReadSetManager)	OT (in bamm.cWrapper)	OUT (in OT)
orientationType (in BM_bamType_C)	OT2Str() (in bamm.cWrapper)

P

P_MEAN (in CT)	pos2 (in BM_linkInfo_C)	printError() (in bamm.bammExceptions)
P_MEAN_OUTLIER (in CT)	PR_PM_PG (in MI)	printLinks() (in BM_fileInfo)
P_MEAN_TRIMMED (in CT)	PR_PM_UG (in MI)	printLinks() (in BamParser)
P_MEDIAN (in CT)	PR_UM_NG (in MI)	printMore() (in BM_linkInfo)
pair (in BM_LinkWalker_C)	printBamTypes() (in BM_fileInfo)	printMore() (in BM_linkPair)
parseBams() (in BamParser)	printBamTypes() (in BamParser)	pythonizeLinks() (in bamm.bamParser)
partnerRead (in BM_mappedRead_C)	printCoverages() (in BM_fileInfo)
pos1 (in BM_linkInfo_C)	printCoverages() (in BamParser)

Q

qual (in BM_mappedRead_C)	qualLen (in BM_mappedRead_C)

R

readLength1 (in BM_linkInfo_C)	removeDatabase() (in BamMaker)	RPI (in bamm.cWrapper)
readLength2 (in BM_linkInfo_C)	reversed1 (in BM_linkInfo_C)	RPI2Str() (in bamm.cWrapper)
ReadSet (in bamm.bamRead)	reversed2 (in BM_linkInfo_C)	RPIConv (in bamm.cWrapper)
ReadSetManager (in bamm.bamRead)	rpi (in BM_mappedRead_C)

S

safeRemove() (in BamMaker)	samtoolsIndex() (in BamMaker)	setResponseQueues() (in ReadSetManager)
SAME (in OT)	SEC (in RPI)	SNGL (in RPI)
sampe() (in BamMaker)	seq (in BM_mappedRead_C)	SNGL_FIR (in RPI)
sampe_to_sorted_indexed_bam() (in BamMaker)	seqId (in BM_mappedRead_C)	SNGL_SEC (in RPI)
samse() (in BamMaker)	seqLen (in BM_mappedRead_C)	stripFaCrud() (in BamScheduler)
samse_to_sorted_indexed_bam() (in BamMaker)	setPrintQueue() (in ReadSetManager)	supporting (in BM_bamType_C)

T

type (in BM_coverageType_C)	types (in BM_bamFile_C)

U

upperCut (in BM_coverageType_C)	UR_NM_NG (in MI)

W

writeChain() (in ReadSet)

_

__credits__ (in bamm.bamExtractor)	__init__() (in BM_linkInfo)	__package__ (in bamm.bamParser)
__credits__ (in bamm.bamFile)	__init__() (in BM_linkPair)	__package__ (in bamm.bamRead)
__credits__ (in bamm.bamLink)	__init__() (in BamMaker)	__package__ (in bamm.bammExceptions)
__credits__ (in bamm.bamMaker)	__init__() (in BamScheduler)	__package__ (in bamm.cWrapper)
__credits__ (in bamm.bamParser)	__init__() (in BamParser)	__str__() (in BM_bamFile)
__credits__ (in bamm.bamRead)	__init__() (in ReadSet)	__str__() (in BM_bamType)
__credits__ (in bamm.bammExceptions)	__init__() (in ReadSetManager)	__str__() (in BM_fileInfo)
__credits__ (in bamm.cWrapper)	__init__() (in CWrapper)	__str__() (in BM_linkInfo)
__email__ (in bamm.bamExtractor)	__maintainer__ (in bamm.bamExtractor)	__str__() (in BM_linkPair)
__email__ (in bamm.bamFile)	__maintainer__ (in bamm.bamFile)	__str__() (in BamMaker)
__email__ (in bamm.bamLink)	__maintainer__ (in bamm.bamLink)	_fields_ (in BM_LinkWalker_C)
__email__ (in bamm.bamMaker)	__maintainer__ (in bamm.bamMaker)	_fields_ (in BM_bamFile_C)
__email__ (in bamm.bamParser)	__maintainer__ (in bamm.bamParser)	_fields_ (in BM_bamType_C)
__email__ (in bamm.bamRead)	__maintainer__ (in bamm.bamRead)	_fields_ (in BM_coverageType_C)
__email__ (in bamm.bammExceptions)	__maintainer__ (in bamm.bammExceptions)	_fields_ (in BM_fileInfo_C)
__email__ (in bamm.cWrapper)	__maintainer__ (in bamm.cWrapper)	_fields_ (in BM_linkInfo_C)
__init__() (in BamExtractor)	__package__ (in bamm)	_fields_ (in BM_linkPair_C)
__init__() (in BM_bamFile)	__package__ (in bamm.bamExtractor)	_fields_ (in BM_mappedRead_C)
__init__() (in BM_bamType)	__package__ (in bamm.bamFile)	_parseOneBam() (in BamParser)
__init__() (in BM_coverageType)	__package__ (in bamm.bamLink)
__init__() (in BM_fileInfo)	__package__ (in bamm.bamMaker)