Index

A

add() (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantHeaderSamples method) (pysam.VariantRecordFilter method) add_hts_options() (pysam.HTSFile method) add_line() (pysam.VariantHeader method) add_meta() (pysam.VariantHeader method) add_record() (pysam.VariantHeader method) add_sample() (pysam.VariantHeader method) add_samples() (pysam.VariantHeader method) aend (pysam.AlignedSegment attribute) alen (pysam.AlignedSegment attribute) aligned_pairs (pysam.AlignedSegment attribute) AlignedSegment (class in pysam)

alignment (pysam.PileupRead attribute) AlignmentFile (class in pysam) AlignmentHeader (class in pysam) allele_indices (pysam.VariantRecordSample attribute) alleles (pysam.VariantRecord attribute) (pysam.VariantRecordSample attribute) alleles_variant_types (pysam.VariantRecord attribute) alts (pysam.VariantHeader attribute) (pysam.VariantRecord attribute) as_dict() (pysam.AlignmentHeader method) asBed (class in pysam) asGTF (class in pysam) asTuple (class in pysam) asVCF (class in pysam) attrs (pysam.VariantHeaderRecord attribute)

B

BAM BCF BED bgzip bin (pysam.AlignedSegment attribute)

blocks (pysam.AlignedSegment attribute) build() (pysam.IndexedReads method) built-in function pysam.samtools.command() pysam.samtools.command.get_messages() pysam.samtools.command.usage()

C

category (pysam.HTSFile attribute) check_index() (pysam.AlignmentFile method) check_truncation() (pysam.HTSFile method) chrom (pysam.VariantRecord attribute) cigar (pysam.AlignedSegment attribute) cigarstring (pysam.AlignedSegment attribute) cigartuples (pysam.AlignedSegment attribute) clear() (pysam.VariantRecordFilter method) (pysam.VariantRecordFormat method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) clear_header() (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) close() (pysam.AlignmentFile method) (pysam.FastaFile method) (pysam.FastxFile method) (pysam.HTSFile method) (pysam.TabixFile method) (pysam.VariantFile method)

closed (pysam.FastaFile attribute) (pysam.FastxFile attribute) (pysam.HTSFile attribute) column compare() (pysam.AlignedSegment method) compression (pysam.HTSFile attribute) contig (pysam.VariantRecord attribute) contigs (pysam.TabixFile attribute) (pysam.VariantHeader attribute) copy() (pysam.AlignmentHeader method) (pysam.VariantFile method) (pysam.VariantHeader method) (pysam.VariantRecord method) count() (pysam.AlignmentFile method) count_coverage() (pysam.AlignmentFile method) CRAM

D

description (pysam.HTSFile attribute) (pysam.VariantMetadata attribute)

E

environment variable PYSAM_PROFILE REF_CACHE REF_PATH

F

faidx FASTA FastaFile (class in pysam) FASTQ FastqProxy (class in pysam) FastxFile (class in pysam) fetch() (pysam.AlignmentFile method) (pysam.FastaFile method) (pysam.TabixFile method) (pysam.VariantFile method) fetching filename (pysam.FastaFile attribute) (pysam.FastxFile attribute) filter (pysam.VariantRecord attribute)

filters (pysam.VariantHeader attribute) find() (pysam.IndexedReads method) find_introns() (pysam.AlignmentFile method) find_introns_slow() (pysam.AlignmentFile method) flag (pysam.AlignedSegment attribute) flush() (pysam.HTSFile method) format (pysam.HTSFile attribute) (pysam.VariantRecord attribute) formats (pysam.VariantHeader attribute) from_dict() (pysam.AlignedSegment class method) (pysam.AlignmentHeader class method) from_references() (pysam.AlignmentHeader class method) from_text() (pysam.AlignmentHeader class method) fromstring() (pysam.AlignedSegment class method)

G

genotype get() (pysam.AlignmentHeader method) (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantHeaderRecord method) (pysam.VariantRecordFilter method) (pysam.VariantRecordFormat method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method) get_aligned_pairs() (pysam.AlignedSegment method) get_blocks() (pysam.AlignedSegment method) get_cigar_stats() (pysam.AlignedSegment method) get_forward_qualities() (pysam.AlignedSegment method) get_forward_sequence() (pysam.AlignedSegment method) get_index_statistics() (pysam.AlignmentFile method) get_mapping_qualities() (pysam.PileupColumn method) get_num_aligned() (pysam.PileupColumn method) get_overlap() (pysam.AlignedSegment method) get_quality_array() (pysam.FastqProxy method) get_query_names() (pysam.PileupColumn method)

get_query_positions() (pysam.PileupColumn method) get_query_qualities() (pysam.PileupColumn method) get_query_sequences() (pysam.PileupColumn method) get_reference_length() (pysam.AlignmentFile method) (pysam.AlignmentHeader method) (pysam.FastaFile method) get_reference_name() (pysam.AlignmentFile method) (pysam.AlignmentHeader method) (pysam.HTSFile method) (pysam.VariantFile method) get_reference_positions() (pysam.AlignedSegment method) get_reference_sequence() (pysam.AlignedSegment method) get_tag() (pysam.AlignedSegment method) get_tags() (pysam.AlignedSegment method) get_tid() (pysam.AlignmentFile method) (pysam.AlignmentHeader method) (pysam.HTSFile method) (pysam.VariantFile method) getrname() (pysam.AlignmentFile method) gettid() (pysam.AlignmentFile method) GTF

H

hard clipped hard clipping has_index() (pysam.AlignmentFile method) has_tag() (pysam.AlignedSegment method)

head() (pysam.AlignmentFile method) header (pysam.TabixFile attribute) header_record (pysam.VariantContig attribute) HTSFile (class in pysam)

I

id (pysam.VariantContig attribute) (pysam.VariantMetadata attribute) (pysam.VariantRecord attribute) indel (pysam.PileupRead attribute) IndexedReads (class in pysam) infer_query_length() (pysam.AlignedSegment method) infer_read_length() (pysam.AlignedSegment method) inferred_length (pysam.AlignedSegment attribute) info (pysam.VariantHeader attribute) (pysam.VariantRecord attribute) is_bam (pysam.HTSFile attribute) is_bcf (pysam.HTSFile attribute) is_closed (pysam.HTSFile attribute) is_cram (pysam.HTSFile attribute) is_del (pysam.PileupRead attribute) is_duplicate (pysam.AlignedSegment attribute) is_forward (pysam.AlignedSegment attribute) is_head (pysam.PileupRead attribute) is_mapped (pysam.AlignedSegment attribute) is_open (pysam.HTSFile attribute) is_open() (pysam.FastaFile method) (pysam.FastxFile method) is_paired (pysam.AlignedSegment attribute) is_proper_pair (pysam.AlignedSegment attribute) is_qcfail (pysam.AlignedSegment attribute) is_read (pysam.HTSFile attribute) is_read1 (pysam.AlignedSegment attribute) is_read2 (pysam.AlignedSegment attribute) is_refskip (pysam.PileupRead attribute) is_reverse (pysam.AlignedSegment attribute) is_sam (pysam.HTSFile attribute) is_secondary (pysam.AlignedSegment attribute) is_supplementary (pysam.AlignedSegment attribute) is_tail (pysam.PileupRead attribute) is_unmapped (pysam.AlignedSegment attribute) is_valid_reference_name() (pysam.HTSFile method) is_valid_tid() (pysam.AlignmentFile method) (pysam.AlignmentHeader method) (pysam.HTSFile method) (pysam.VariantFile method)

is_vcf (pysam.HTSFile attribute) is_write (pysam.HTSFile attribute) isize (pysam.AlignedSegment attribute) items() (pysam.AlignmentHeader method) (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantHeaderRecord method) (pysam.VariantRecordFilter method) (pysam.VariantRecordFormat method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method) iteritems() (pysam.AlignmentHeader method) (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantHeaderRecord method) (pysam.VariantRecordFilter method) (pysam.VariantRecordFormat method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method) iterkeys() (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantHeaderRecord method) (pysam.VariantRecordFilter method) (pysam.VariantRecordFormat method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method) itervalues() (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantHeaderRecord method) (pysam.VariantRecordFilter method) (pysam.VariantRecordFormat method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method)

K

key (pysam.VariantHeaderRecord attribute) keys() (pysam.AlignmentHeader method) (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantHeaderRecord method) (pysam.VariantRecordFilter method) (pysam.VariantRecordFormat method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method)

L

length (pysam.VariantContig attribute) lengths (pysam.AlignmentFile attribute) (pysam.AlignmentHeader attribute) (pysam.FastaFile attribute)

level (pysam.PileupRead attribute)

M

mapped (pysam.AlignmentFile attribute) mapping_quality (pysam.AlignedSegment attribute) mapq (pysam.AlignedSegment attribute) mate() (pysam.AlignmentFile method) mate_is_forward (pysam.AlignedSegment attribute) mate_is_mapped (pysam.AlignedSegment attribute)

mate_is_reverse (pysam.AlignedSegment attribute) mate_is_unmapped (pysam.AlignedSegment attribute) merge() (pysam.VariantHeader method) modified_bases (pysam.AlignedSegment attribute) modified_bases_forward (pysam.AlignedSegment attribute) mpos (pysam.AlignedSegment attribute) mrnm (pysam.AlignedSegment attribute)

N

n (pysam.PileupColumn attribute) name (pysam.FastqProxy attribute) (pysam.VariantContig attribute) (pysam.VariantMetadata attribute) (pysam.VariantRecordSample attribute) new_record() (pysam.VariantFile method) (pysam.VariantHeader method) next_reference_id (pysam.AlignedSegment attribute)

next_reference_name (pysam.AlignedSegment attribute) next_reference_start (pysam.AlignedSegment attribute) nocoordinate (pysam.AlignmentFile attribute) nreferences (pysam.AlignmentFile attribute) (pysam.AlignmentHeader attribute) (pysam.FastaFile attribute) nsegments (pysam.PileupColumn attribute) number (pysam.VariantMetadata attribute)

O

open() (pysam.VariantFile method)

opt() (pysam.AlignedSegment method) overlap() (pysam.AlignedSegment method)

P

parse_region() (pysam.HTSFile method) phased (pysam.VariantRecordSample attribute) pileup pileup() (pysam.AlignmentFile method) PileupColumn (class in pysam) PileupRead (class in pysam) pileups (pysam.PileupColumn attribute) pnext (pysam.AlignedSegment attribute) pop() (pysam.VariantHeaderRecord method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method)

pos (pysam.AlignedSegment attribute) (pysam.PileupColumn attribute) (pysam.VariantRecord attribute) positions (pysam.AlignedSegment attribute) pysam.samtools.command() built-in function pysam.samtools.command.get_messages() built-in function pysam.samtools.command.usage() built-in function PYSAM_PROFILE

Q

qend (pysam.AlignedSegment attribute) qlen (pysam.AlignedSegment attribute) qname (pysam.AlignedSegment attribute) qqual (pysam.AlignedSegment attribute) qstart (pysam.AlignedSegment attribute) qual (pysam.AlignedSegment attribute) (pysam.VariantRecord attribute) quality (pysam.FastqProxy attribute) query (pysam.AlignedSegment attribute) query_alignment_end (pysam.AlignedSegment attribute) query_alignment_length (pysam.AlignedSegment attribute)

query_alignment_qualities (pysam.AlignedSegment attribute) query_alignment_qualities_str (pysam.AlignedSegment attribute) query_alignment_sequence (pysam.AlignedSegment attribute) query_alignment_start (pysam.AlignedSegment attribute) query_length (pysam.AlignedSegment attribute) query_name (pysam.AlignedSegment attribute) query_position (pysam.PileupRead attribute) query_position_or_next (pysam.PileupRead attribute) query_qualities (pysam.AlignedSegment attribute) query_qualities_str (pysam.AlignedSegment attribute) query_sequence (pysam.AlignedSegment attribute)

R

record (pysam.VariantMetadata attribute) records (pysam.VariantHeader attribute) ref (pysam.VariantRecord attribute) REF_CACHE REF_PATH reference reference_end (pysam.AlignedSegment attribute) reference_id (pysam.AlignedSegment attribute) (pysam.PileupColumn attribute) reference_length (pysam.AlignedSegment attribute) reference_name (pysam.AlignedSegment attribute) (pysam.PileupColumn attribute) reference_pos (pysam.PileupColumn attribute) reference_start (pysam.AlignedSegment attribute) references (pysam.AlignmentFile attribute) (pysam.AlignmentHeader attribute) (pysam.FastaFile attribute)

region remove() (pysam.VariantHeaderRecord method) remove_header() (pysam.VariantContig method) (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantMetadata method) reset() (pysam.HTSFile method) (pysam.VariantFile method) rid (pysam.VariantRecord attribute) rlen (pysam.AlignedSegment attribute) (pysam.VariantRecord attribute) rname (pysam.AlignedSegment attribute) rnext (pysam.AlignedSegment attribute)

S

SAM sam file samples (pysam.VariantHeader attribute) (pysam.VariantRecord attribute) seek() (pysam.HTSFile method) seq (pysam.AlignedSegment attribute) sequence (pysam.FastqProxy attribute) set_min_base_quality() (pysam.PileupColumn method)

set_tag() (pysam.AlignedSegment method) set_tags() (pysam.AlignedSegment method) setTag() (pysam.AlignedSegment method) soft clipped soft clipping start (pysam.VariantRecord attribute) stop (pysam.VariantRecord attribute) subset_samples() (pysam.VariantFile method)

T

tabix tabix file tabix row tabix_compress() (in module pysam) tabix_index() (in module pysam) tabix_iterator() (in module pysam) TabixFile (class in pysam) tags (pysam.AlignedSegment attribute) TAM target tell() (pysam.HTSFile method) template_length (pysam.AlignedSegment attribute)

text (pysam.AlignmentFile attribute) tid (pysam.AlignedSegment attribute) (pysam.PileupColumn attribute) tlen (pysam.AlignedSegment attribute) to_dict() (pysam.AlignedSegment method) (pysam.AlignmentHeader method) to_string() (pysam.AlignedSegment method) tostring() (pysam.AlignedSegment method) translate() (pysam.VariantRecord method) type (pysam.VariantHeaderRecord attribute) (pysam.VariantMetadata attribute)

U

unmapped (pysam.AlignmentFile attribute) update() (pysam.VariantHeaderRecord method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method)

V

value (pysam.VariantHeaderRecord attribute) values() (pysam.AlignmentHeader method) (pysam.VariantHeaderContigs method) (pysam.VariantHeaderMetadata method) (pysam.VariantHeaderRecord method) (pysam.VariantRecordFilter method) (pysam.VariantRecordFormat method) (pysam.VariantRecordInfo method) (pysam.VariantRecordSample method) (pysam.VariantRecordSamples method) VariantContig (class in pysam) VariantFile (class in pysam) VariantHeader (class in pysam) VariantHeaderContigs (class in pysam)

VariantHeaderMetadata (class in pysam) VariantHeaderRecord (class in pysam) VariantHeaderRecords (class in pysam) VariantHeaderSamples (class in pysam) VariantMetadata (class in pysam) VariantRecord (class in pysam) VariantRecordFilter (class in pysam) VariantRecordFormat (class in pysam) VariantRecordInfo (class in pysam) VariantRecordSample (class in pysam) VariantRecordSamples (class in pysam) VCF version (pysam.HTSFile attribute) (pysam.VariantHeader attribute)

W

write() (pysam.AlignmentFile method) (pysam.VariantFile method)