`bio.bam`¶

Source code: bio/bam.seq

bio.bam.BAM_FPAIRED¶

bio.bam.BAM_FPROPER_PAIR¶

bio.bam.BAM_FUNMAP¶

bio.bam.BAM_FMUNMAP¶

bio.bam.BAM_FREVERSE¶

bio.bam.BAM_FMREVERSE¶

bio.bam.BAM_FREAD1¶

bio.bam.BAM_FREAD2¶

bio.bam.BAM_FSECONDARY¶

bio.bam.BAM_FQCFAIL¶

bio.bam.BAM_FDUP¶

bio.bam.BAM_FSUPPLEMENTARY¶

bio.bam.AUX_TYPE_INT8¶

bio.bam.AUX_TYPE_UINT8¶

bio.bam.AUX_TYPE_INT16¶

bio.bam.AUX_TYPE_UINT16¶

bio.bam.AUX_TYPE_INT32¶

bio.bam.AUX_TYPE_UINT32¶

bio.bam.AUX_TYPE_FLOAT¶

bio.bam.AUX_TYPE_DOUBLE¶

bio.bam.AUX_TYPE_CHAR¶

bio.bam.AUX_TYPE_STRING¶

bio.bam.AUX_TYPE_ARRAY¶

bio.bam.AUX_TYPE_INT¶

class bio.bam.SAMAux¶

Properties:

tag_type¶

String representing the type of this tag.

“int”: use i property for int value

“float”: use f property for float value

“char”: use A property for byte value

“string”: use Z property for string value

“Array[int]”: use B_len for array length and either B2i(index) to access elements

“Array[float]”: use B_len for array length and either B2f(index) to access elements

i¶

Int value of this tag

f¶

Float value of this tag

A¶

Byte value of this tag

Z¶

String value of this tag

B_len¶

Array length of this tag

Magic methods:

__bool__()

__str__()

__len__()

Methods:

B2i(idx: int)¶

`idx`th element of integer array comprising this tag

B2f(idx: int)¶

`idx`th element of float array comprising this tag

class bio.bam.SAMRecord¶

Properties:

name¶

Read name of this record

query_name¶

Alias of name

read¶

seq¶

Record sequence

qual¶

Record quality string

cigar¶

Record CIGAR

tid¶

Record contig ID

flag¶

Record flag

pos¶

Record position (0-based)

locus¶

Record Locus consisting of tid and pos

mate_tid¶

Contig ID in mate’s record

mate_pos¶

Position in mate’s record (0-based)

mate_locus¶

Record Locus of mate’s record consisting of mate_tid and mate_pos

mapq¶

Record’s mapping quality

insert_size¶

Record’s insert size

paired¶

Whether this record is paired

proper_pair¶

Whether this record and its pair form a proper pair

unmapped¶

Whether this record is unmapped

mate_unmapped¶

Whether mate’s record is unmapped

reversed¶

Whether this record is reverse complemented on the reference

mate_reversed¶

Whether this record’s mate is reverse complemented on the reference

read1¶

Whether this is the first read in the pair

read2¶

Whether this is the second read in the pair

secondary¶

Whether this is a seconday alignment

qc_fail¶

Whether this record failed quality control checks

duplicate¶

Whether this record is marked as a duplicate

supplementary¶

Whether this record is supplementary

endpos¶

The rightmost base position of an alignment on the reference genome

Magic methods:

__init__(htslib_record: _bam1_t)

Methods:

aux(tag: str)¶

Returns the auxiliary tag with the specified key.

class bio.bam.BAMReader¶

Magic methods:

__init__(path: str, region: str, copy: bool)

__blocks__(size: int)

__seqs__()

__iter__()

__enter__()

__exit__()

Methods:

seek(region: str)¶

close()¶

contigs()¶

contig(rid: int)¶

class bio.bam.SAMReader¶

Magic methods:

__init__(path: str, copy: bool)

__seqs__()

__iter__()

__blocks__(size: int)

__enter__()

__exit__()

Methods:

close()¶

contigs()¶

contig(rid: int)¶

bio.bam.CRAMReader¶

bio.bam.SAM(path: str, copy: bool = True)¶

bio.bam.BAM(path: str, region: str = '.', copy: bool = True)¶

bio.bam.CRAM(path: str, region: str = '.', copy: bool = True)¶

bio.bam¶

`bio.bam`¶