bio.bam
¶
Source code: bio/bam.seq
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bio.bam.
BAM_FPAIRED
¶
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bio.bam.
BAM_FPROPER_PAIR
¶
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bio.bam.
BAM_FUNMAP
¶
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bio.bam.
BAM_FMUNMAP
¶
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bio.bam.
BAM_FREVERSE
¶
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bio.bam.
BAM_FMREVERSE
¶
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bio.bam.
BAM_FREAD1
¶
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bio.bam.
BAM_FREAD2
¶
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bio.bam.
BAM_FSECONDARY
¶
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bio.bam.
BAM_FQCFAIL
¶
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bio.bam.
BAM_FDUP
¶
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bio.bam.
BAM_FSUPPLEMENTARY
¶
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bio.bam.
AUX_TYPE_INT8
¶
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bio.bam.
AUX_TYPE_UINT8
¶
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bio.bam.
AUX_TYPE_INT16
¶
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bio.bam.
AUX_TYPE_UINT16
¶
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bio.bam.
AUX_TYPE_INT32
¶
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bio.bam.
AUX_TYPE_UINT32
¶
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bio.bam.
AUX_TYPE_FLOAT
¶
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bio.bam.
AUX_TYPE_DOUBLE
¶
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bio.bam.
AUX_TYPE_CHAR
¶
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bio.bam.
AUX_TYPE_STRING
¶
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bio.bam.
AUX_TYPE_ARRAY
¶
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bio.bam.
AUX_TYPE_INT
¶
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type
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 eitherB2i(index)
to access elements“array[float]”: use
B_len
for array length and eitherB2i(index)
to access elements
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i
¶ Int value of this tag
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f
¶ Float value of this tag
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A
¶ Byte value of this tag
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Z
¶ String value of this tag
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B_len
¶ Array length of this tag
Magic methods:
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__bool__
()
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__str__
()
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__len__
()
Methods:
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class
bio.bam.
SAMRecord
¶ Properties:
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name
¶ Read name of this record
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query_name
¶ Alias of name
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read
¶
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seq
¶ Record sequence
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qual
¶ Record quality string
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cigar
¶ Record CIGAR
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tid
¶ Record contig ID
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flag
¶ Record flag
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pos
¶ Record position (0-based)
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locus
¶ Record Locus consisting of tid and pos
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mate_tid
¶ Contig ID in mate’s record
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mate_pos
¶ Position in mate’s record (0-based)
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mate_locus
¶ Record Locus of mate’s record consisting of mate_tid and mate_pos
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mapq
¶ Record’s mapping quality
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insert_size
¶ Record’s insert size
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paired
¶ Whether this record is paired
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proper_pair
¶ Whether this record and its pair form a proper pair
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unmapped
¶ Whether this record is unmapped
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mate_unmapped
¶ Whether mate’s record is unmapped
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reversed
¶ Whether this record is reverse complemented on the reference
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mate_reversed
¶ Whether this record’s mate is reverse complemented on the reference
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read1
¶ Whether this is the first read in the pair
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read2
¶ Whether this is the second read in the pair
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secondary
¶ Whether this is a seconday alignment
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qc_fail
¶ Whether this record failed quality control checks
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duplicate
¶ Whether this record is marked as a duplicate
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supplementary
¶ Whether this record is supplementary
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endpos
¶ The rightmost base position of an alignment on the reference genome
Magic methods:
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__init__
(htslib_record: _bam1_t)
Methods:
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aux
(tag: str)¶ Returns the auxiliary tag with the specified key.
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class
bio.bam.
BAMReader
¶ Magic methods:
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__init__
(path: str, region: str, copy: bool)
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__blocks__
(size: int)
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__seqs__
()
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__iter__
()
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__enter__
()
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__exit__
()
Methods:
-
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class
bio.bam.
SAMReader
¶ Magic methods:
-
__init__
(path: str, copy: bool)
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__seqs__
()
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__iter__
()
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__blocks__
(size: int)
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__enter__
()
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__exit__
()
Methods:
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bio.bam.
SAM
(path: str, copy: bool = True)¶
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bio.bam.
BAM
(path: str, region: str = '.', copy: bool = True)¶
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bio.bam.
CRAM
(path: str, region: str = '.', copy: bool = True)¶