Index

Symbols

-a <minaqual>, --a=<minaqual> htseq-count command line option -g <gamma>, --gamma=<gamma> htseq-qa command line option -h, --help htseq-count command line option htseq-qa command line option -i <id attribute>, --idattr=<id attribute> htseq-count command line option -m <mode>, --mode=<mode> htseq-count command line option -m, --maxqual htseq-qa command line option -n, --nosplit htseq-qa command line option

-o <outfile>, --outfile=<outfile> htseq-qa command line option -o <samout>, --samout=<samout> htseq-count command line option -q, --quiet htseq-count command line option -r <readlen>, --readlength=<readlen> htseq-qa command line option -s <yes, no or reverse>, --stranded=<yes, no, or reverse> htseq-count command line option -t <feature type>, --type=<feature type> htseq-count command line option -t <type>, --type=<type> htseq-qa command line option

_

__version__ (in module HTSeq)

A

add_chrom() (HTSeq.GenomicArray method) aligned (HTSeq.Alignment attribute) Alignment (class in HTSeq) AlignmentWithSequenceReversal (class in HTSeq) alt (HTSeq.VariantCall attribute)

apply() (HTSeq.ChromVector method) aQual (HTSeq.SAM_Alignment attribute) attr (HTSeq.GenomicFeature attribute) auto_add_chroms (HTSeq.GenomicArray attribute)

B

BAM_Reader (class in HTSeq) BowtieAlignment (class in HTSeq)

BowtieReader (class in HTSeq) bundle_multiple_alignments() (in module HTSeq)

C

check() (HTSeq.CigarOperation method) chrom (HTSeq.GenomicInterval attribute) (HTSeq.VariantCall attribute) chrom_vectors (HTSeq.GenomicArray attribute)

cigar (HTSeq.SAM_Alignment attribute) CigarOperation (class in HTSeq) contains() (HTSeq.GenomicInterval method)

D

descr (HTSeq.Sequence attribute)

E

end (HTSeq.GenomicInterval attribute) end_as_pos (HTSeq.GenomicInterval attribute) end_d (HTSeq.GenomicInterval attribute)

end_d_as_pos (HTSeq.GenomicInterval attribute) extend_to_include() (HTSeq.GenomicInterval method)

F

failed_platform_qc (HTSeq.SAM_Alignment attribute) FastaReader (class in HTSeq) FastqReader (class in HTSeq) FileOrSequence (class in HTSeq)

filter (HTSeq.VariantCall attribute) format (HTSeq.VariantCall attribute) fos (HTSeq.FileOrSequence attribute) frame (HTSeq.GenomicFeature attribute)

G

GenomicArray (class in HTSeq) GenomicArrayOfSets (class in HTSeq) GenomicFeature (class in HTSeq) GenomicInterval (class in HTSeq) GenomicInterval_from_directional() (in module HTSeq) GenomicPosition (class in HTSeq)

get_gff_line() (HTSeq.GenomicFeature method) get_line_number_string() (HTSeq.FileOrSequence method) get_reverse_complement() (HTSeq.Sequence method) get_sam_line() (HTSeq.SAM_Alignment method) GFF_Reader (class in HTSeq)

H

htseq-count command line option -a <minaqual>, --a=<minaqual> -h, --help -i <id attribute>, --idattr=<id attribute> -m <mode>, --mode=<mode> -o <samout>, --samout=<samout> -q, --quiet -s <yes, no or reverse>, --stranded=<yes, no, or reverse> -t <feature type>, --type=<feature type>

htseq-qa command line option -g <gamma>, --gamma=<gamma> -h, --help -m, --maxqual -n, --nosplit -o <outfile>, --outfile=<outfile> -r <readlen>, --readlength=<readlen> -t <type>, --type=<type>

I

id (HTSeq.VariantCall attribute) inferred_insert_size (HTSeq.SAM_Alignment attribute) info (HTSeq.VariantCall attribute)

interval (HTSeq.GenomicFeature attribute) is_contained_in() (HTSeq.GenomicInterval method) iv (HTSeq.Alignment attribute)

L

length (HTSeq.GenomicInterval attribute)

line_no (HTSeq.FileOrSequence attribute)

M

mate_aligned (HTSeq.SAM_Alignment attribute) mate_start (HTSeq.SAM_Alignment attribute)

metadata (HTSeq.GFF_Reader attribute) (HTSeq.VCF_Reader attribute)

N

name (HTSeq.GenomicFeature attribute) (HTSeq.Sequence attribute) nomatch_code (HTSeq.SolexaExportAlignment attribute)

nor_primary_alignment (HTSeq.SAM_Alignment attribute)

O

optional_field (HTSeq.SAM_Alignment attribute) optional_fields (HTSeq.SAM_Alignment attribute)

overlaps() (HTSeq.GenomicInterval method)

P

pair_SAM_alignments() (in module HTSeq) paired_end (HTSeq.Alignment attribute) parse_GFF_attribute_string() (in module HTSeq) passed_filter (HTSeq.SolexaExportAlignment attribute)

pcr_or_optical_duplicate (HTSeq.SAM_Alignment attribute) pe_which (HTSeq.SAM_Alignment attribute) pos (HTSeq.VariantCall attribute) (in module HTSeq) proper_pair (HTSeq.SAM_Alignment attribute)

Q

qual (HTSeq.SequenceWithQuality attribute) (HTSeq.VariantCall attribute) qualstr (HTSeq.SequenceWithQuality attribute)

query_from (HTSeq.CigarOperation attribute) query_to (HTSeq.CigarOperation attribute)

R

read (HTSeq.Alignment attribute) read_as_aligned (HTSeq.AlignmentWithSequenceReversal attribute) read_as_sequenced (HTSeq.AlignmentWithSequenceReversal attribute)

ref (HTSeq.VariantCall attribute) ref_iv (HTSeq.CigarOperation attribute) reserved (HTSeq.BowtieAlignment attribute)

S

SAM_Alignment (class in HTSeq) SAM_Reader (class in HTSeq) samples (HTSeq.VariantCall attribute) score (HTSeq.GenomicFeature attribute) seq (HTSeq.Sequence attribute) Sequence (class in HTSeq) SequenceWithQualities (class in HTSeq) size (HTSeq.CigarOperation attribute) SolexaExportAlignment (class in HTSeq) SolexaExportReader (class in HTSeq)

source (HTSeq.GenomicFeature attribute) start (HTSeq.GenomicInterval attribute) start_as_pos (HTSeq.GenomicInterval attribute) start_d (HTSeq.GenomicInterval attribute) start_d_as_pos (HTSeq.GenomicInterval attribute) steps() (HTSeq.ChromVector method) (HTSeq.GenomicArray method) strand (HTSeq.GenomicInterval attribute) stranded (HTSeq.GenomicArray attribute) substitutions (HTSeq.BowtieAlignment attribute)

T

trim_left_end() (HTSeq.Sequence method) trim_left_end_with_quals() (HTSeq.SequenceWithQualities method) trim_right_end() (HTSeq.Sequence method)

trim_right_end_with_quals() (HTSeq.SequenceWithQualities method) type (HTSeq.CigarOperation attribute) (HTSeq.GenomicFeature attribute) typecode (HTSeq.GenomicArray attribute)

V

VariantCall (class in HTSeq) VariantCall.unpack_info() (in module HTSeq) VCF_Reader (class in HTSeq)

VCF_Reader.make_info_dict() (in module HTSeq) VCF_Reader.parse_meta() (in module HTSeq)

W

write_bedgraph_file() (HTSeq.GenomicArray method)

write_to_fastq_file() (HTSeq.SequenceWithQuality method)

X

xrange() (HTSeq.GenomicInterval method)

xrange_d() (HTSeq.GenomicInterval method)