Index

A

adjacency (class in mclumi.deduplicate.monomer.Adjacency) (class in mclumi.network.Adjacency)

B

bamids() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method)

build (class in mclumi.deduplicate.monomer.Build) bycol() (mclumi.align.Read.read method)

C

call() (mclumi.trim.Fixed.fixed method) cc (class in mclumi.network.CC) cc() (mclumi.deduplicate.monomer.Cluster.cluster method) ccnx() (mclumi.deduplicate.monomer.Cluster.cluster method) check() (mclumi.util.Console.console method)

cluster (class in mclumi.deduplicate.monomer.Cluster) cluster() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) console (class in mclumi.util.Console) correct() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method)

D

decompose() (mclumi.deduplicate.monomer.Adjacency.adjacency method) (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method) (mclumi.deduplicate.monomer.Directional.directional method) (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) dedupBasic (class in mclumi.deduplicate.monomer.DedupBasic) dedupGene (class in mclumi.deduplicate.monomer.DedupGene) dedupPos (class in mclumi.deduplicate.monomer.DedupPos) dedupSC (class in mclumi.deduplicate.monomer.DedupSC) deque() (mclumi.network.CC.cc method)

dfclusters() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) dfs() (mclumi.deduplicate.monomer.Directional.directional method) dict() (mclumi.network.Adjacency.adjacency method) dictTo2d() (mclumi.deduplicate.monomer.Directional.directional method) diffDedupReadCountPos() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method) diffDedupUniqCountPos() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method) directional (class in mclumi.deduplicate.monomer.Directional)

E

ed_list_() (mclumi.deduplicate.monomer.Build.build method) edave() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method) edge (class in mclumi.network.Edge) eds_() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method)

evaluate() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method) excel() (mclumi.util.Reader.reader method) (mclumi.util.Writer.writer method)

F

filter (class in mclumi.trim.Filter) fixed (class in mclumi.trim.Fixed) folder (class in mclumi.util.Folder) formatApvsDisapv() (mclumi.deduplicate.monomer.Directional.directional method)

formatCCS() (mclumi.deduplicate.monomer.Directional.directional method) fromdf() (mclumi.network.Edge.edge method) fromgz() (mclumi.fastq.Read.read method) fromlist() (mclumi.network.Edge.edge method)

G

general() (mclumi.util.Hamming.hamming method) generic() (mclumi.util.Reader.reader method) (mclumi.util.Writer.writer method) get() (mclumi.util.Single.single method) getEleTrimmed() (mclumi.util.Single.single method) getLisTrimmed() (mclumi.util.Single.single method)

glen (mclumi.network.Adjacency.adjacency property) (mclumi.network.Edge.edge property) graph (mclumi.network.Adjacency.adjacency property) (mclumi.network.Edge.edge property) graph_cc_adj() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) graph_mapped (mclumi.network.Adjacency.adjacency property) (mclumi.network.Edge.edge property)

H

hamming (class in mclumi.util.Hamming)

hash() (mclumi.network.Adjacency.adjacency method)

I

is_sv (mclumi.align.Write.write property)

K

key_mapped (mclumi.network.Adjacency.adjacency property) (mclumi.network.Edge.edge property)

keymap() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) keyToNode() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method)

L

length() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method)

list() (mclumi.network.Adjacency.adjacency method)

M

main() (in module mclumi.Main) map() (mclumi.network.Adjacency.adjacency method) (mclumi.network.Edge.edge method) markovClustering (class in mclumi.deduplicate.monomer.MarkovClustering) markSingleUMI() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method) matrix() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) (mclumi.network.Adjacency.adjacency method) maxval_ed() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) maxval_ed_() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) maxval_val() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) maxval_val_() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method) mclumi module mclumi.align module mclumi.align.Read module mclumi.align.Write module mclumi.deduplicate module mclumi.deduplicate.monomer module mclumi.deduplicate.monomer.Adjacency module mclumi.deduplicate.monomer.Build module mclumi.deduplicate.monomer.Cluster module mclumi.deduplicate.monomer.DedupBasic module mclumi.deduplicate.monomer.DedupGene module mclumi.deduplicate.monomer.DedupPos module mclumi.deduplicate.monomer.DedupSC module mclumi.deduplicate.monomer.Directional module mclumi.deduplicate.monomer.MarkovClustering module mclumi.fastq module mclumi.fastq.Read module mclumi.fastq.Write module mclumi.Main module mclumi.network module mclumi.network.Adjacency module mclumi.network.CC module mclumi.network.Edge module mclumi.Path module mclumi.trim module mclumi.trim.Filter module

mclumi.trim.Fixed module mclumi.trim.Reader module mclumi.trim.SeqRuleOut module mclumi.trim.Template module mclumi.trim.UMIRuleOut module mclumi.util module mclumi.util.Console module mclumi.util.Folder module mclumi.util.Hamming module mclumi.util.Number module mclumi.util.Reader module mclumi.util.Single module mclumi.util.Writer module method() (mclumi.trim.Filter.filter method) module mclumi mclumi.align mclumi.align.Read mclumi.align.Write mclumi.deduplicate mclumi.deduplicate.monomer mclumi.deduplicate.monomer.Adjacency mclumi.deduplicate.monomer.Build mclumi.deduplicate.monomer.Cluster mclumi.deduplicate.monomer.DedupBasic mclumi.deduplicate.monomer.DedupGene mclumi.deduplicate.monomer.DedupPos mclumi.deduplicate.monomer.DedupSC mclumi.deduplicate.monomer.Directional mclumi.deduplicate.monomer.MarkovClustering mclumi.fastq mclumi.fastq.Read mclumi.fastq.Write mclumi.Main mclumi.network mclumi.network.Adjacency mclumi.network.CC mclumi.network.Edge mclumi.Path mclumi.trim mclumi.trim.Filter mclumi.trim.Fixed mclumi.trim.Reader mclumi.trim.SeqRuleOut mclumi.trim.Template mclumi.trim.UMIRuleOut mclumi.util mclumi.util.Console mclumi.util.Folder mclumi.util.Hamming mclumi.util.Number mclumi.util.Reader mclumi.util.Single mclumi.util.Writer

N

nodes (mclumi.network.Edge.edge property)

number (class in mclumi.util.Number)

O

osmkdir() (mclumi.util.Folder.folder method)

P

paired() (mclumi.trim.Filter.filter method) pcrnum() (mclumi.deduplicate.monomer.Build.build method) (mclumi.trim.Reader.reader method)

print() (mclumi.util.Console.console method)

R

read (class in mclumi.align.Read) (class in mclumi.fastq.Read) reader (class in mclumi.trim.Reader) (class in mclumi.util.Reader)

root_dict() (in module mclumi.Path) rvredanduncy (mclumi.network.Edge.edge property)

S

seqRuleOut (class in mclumi.trim.SeqRuleOut) sequential() (mclumi.trim.SeqRuleOut.seqRuleOut method) (mclumi.trim.UMIRuleOut.umiRuleOut method) set() (mclumi.network.Adjacency.adjacency method) (mclumi.network.CC.cc method)

single (class in mclumi.util.Single) singleStart() (mclumi.trim.Filter.filter method) sort_vals() (mclumi.deduplicate.monomer.MarkovClustering.markovClustering method)

T

template (class in mclumi.trim.Template) to() (in module mclumi.Path) toAdjacencyDict() (mclumi.network.Edge.edge method) tobam() (mclumi.align.Write.write method) todf() (mclumi.align.Read.read method) (mclumi.trim.Reader.reader method) (mclumi.trim.Template.template method)

todf11() (mclumi.align.Read.read method) todf11_depr() (mclumi.align.Read.read method) todict() (mclumi.util.Single.single method) toEdgeList() (mclumi.network.Adjacency.adjacency method) togz() (mclumi.fastq.Write.write method) (mclumi.trim.Template.template method) trim() (mclumi.util.Single.single static method)

U

umi_tools() (mclumi.deduplicate.monomer.Adjacency.adjacency method) (mclumi.deduplicate.monomer.Directional.directional method) umi_tools_() (mclumi.deduplicate.monomer.Adjacency.adjacency method) (mclumi.deduplicate.monomer.Directional.directional method) umimax() (mclumi.deduplicate.monomer.DedupBasic.dedupBasic method) (mclumi.deduplicate.monomer.DedupGene.dedupGene method) (mclumi.deduplicate.monomer.DedupPos.dedupPos method) (mclumi.deduplicate.monomer.DedupSC.dedupSC method)

umiRuleOut (class in mclumi.trim.UMIRuleOut) uniform() (mclumi.util.Number.number method)

V

verbose (mclumi.util.Console.console property)

W

write (class in mclumi.align.Write) (class in mclumi.fastq.Write)

writer (class in mclumi.util.Writer)