Index

_

__init__() (itsxpress.SeqSample.Dedup method) (itsxpress.SeqSample.ItsPosition method) (itsxpress.SeqSample.SeqSample method) (itsxpress.SeqSample.SeqSampleNotPaired method) (itsxpress.SeqSample.SeqSamplePairedNotInterleaved method) _check_fastqs() (in module itsxpress.main) _check_total_reads() (in module itsxpress.main)

_get_paired_seq_generator() (itsxpress.SeqSample.Dedup method) _get_trimmed_seq_generator() (itsxpress.SeqSample.Dedup method) _is_paired() (in module itsxpress.main) _logger_setup() (in module itsxpress.main) _merge_reads() (itsxpress.SeqSample.SeqSamplePairedNotInterleaved method) _score() (itsxpress.SeqSample.ItsPosition method) _search() (itsxpress.SeqSample.SeqSample method)

C

cluster() (itsxpress.SeqSample.SeqSample method) create_paired_trimmed_seqs() (itsxpress.SeqSample.Dedup method)

create_runtime_hmm() (in module itsxpress.main) create_temp_directory() (in module itsxpress.main) create_trimmed_seqs() (itsxpress.SeqSample.Dedup method)

D

ddict (itsxpress.SeqSample.ItsPosition attribute) Dedup (class in itsxpress.SeqSample)

deduplicate() (itsxpress.SeqSample.SeqSample method) dom_file (itsxpress.SeqSample.SeqSample attribute) domtable (itsxpress.SeqSample.ItsPosition attribute)

F

fastq (itsxpress.SeqSample.Dedup attribute) (itsxpress.SeqSample.SeqSample attribute)

fastq2 (itsxpress.SeqSample.Dedup attribute) (itsxpress.SeqSample.SeqSample attribute)

G

get_position() (itsxpress.SeqSample.ItsPosition method)

I

ItsPosition (class in itsxpress.SeqSample) itsxpress module itsxpress.definitions module

itsxpress.main module itsxpress.SeqSample module

L

leftprefix (itsxpress.SeqSample.ItsPosition attribute)

M

main() (in module itsxpress.main) matchdict (itsxpress.SeqSample.Dedup attribute) module itsxpress itsxpress.definitions itsxpress.main itsxpress.SeqSample

myparser() (in module itsxpress.main)

O

orient_reads() (itsxpress.SeqSample.SeqSample method)

P

parse() (itsxpress.SeqSample.Dedup method) (itsxpress.SeqSample.ItsPosition method)

R

r1 (itsxpress.SeqSample.SeqSample attribute) read_file() (in module itsxpress.main) region (itsxpress.SeqSample.ItsPosition attribute)

rep_file (itsxpress.SeqSample.Dedup attribute) (itsxpress.SeqSample.SeqSample attribute) restricted_float() (in module itsxpress.main) rightprefix (itsxpress.SeqSample.ItsPosition attribute)

S

seq_file (itsxpress.SeqSample.Dedup attribute) (itsxpress.SeqSample.SeqSample attribute)

SeqSample (class in itsxpress.SeqSample) SeqSampleNotPaired (class in itsxpress.SeqSample) SeqSamplePairedNotInterleaved (class in itsxpress.SeqSample)

T

tempdir (itsxpress.SeqSample.SeqSample attribute)

U

uc_file (itsxpress.SeqSample.Dedup attribute) (itsxpress.SeqSample.SeqSample attribute)