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Heng Li 2017-09-16 22:36:19 -04:00
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python/README.rst
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@ -52,71 +52,71 @@ Class minimap2.Aligner
Arguments: Arguments:
* `fn_idx_in`: index or sequence file name. Minimap2 automatically tests the * **fn_idx_in**: index or sequence file name. Minimap2 automatically tests the
file type. If a sequence file is provided, minimap2 builds an index. The file type. If a sequence file is provided, minimap2 builds an index. The
sequence file can be optionally gzip'd. sequence file can be optionally gzip'd.
* `preset`: minimap2 preset. Currently, minimap2 supports the following * **preset**: minimap2 preset. Currently, minimap2 supports the following
presets: `sr` for single-end short reads; `map-pb` for PacBio presets: **sr** for single-end short reads; **map-pb** for PacBio
read-to-reference mapping; `map-ont` for Oxford Nanopore read mapping; read-to-reference mapping; **map-ont** for Oxford Nanopore read mapping;
`splice` for long-read spliced alignment; `asm5` for assembly-to-assembly **splice** for long-read spliced alignment; **asm5** for assembly-to-assembly
alignment; `asm10` for full genome alignment of closely related species. Note alignment; **asm10** for full genome alignment of closely related species. Note
that the Python module does not support all-vs-all read overlapping. that the Python module does not support all-vs-all read overlapping.
* `k`: k-mer length, no larger than 28 * **k**: k-mer length, no larger than 28
* `w`: minimizer window size, no larger than 255 * **w**: minimizer window size, no larger than 255
* `min_cnt`: mininum number of minimizers on a chain * **min_cnt**: mininum number of minimizers on a chain
* `min_chain_score`: minimum chaing score * **min_chain_score**: minimum chaing score
* `bw`: chaining and alignment band width * **bw**: chaining and alignment band width
* `best_n`: max number of alignments to return * **best_n**: max number of alignments to return
* `n_threads`: number of indexing threads; 3 by default * **n_threads**: number of indexing threads; 3 by default
* `fn_idx_out`: name of file to which the index is written * **fn_idx_out**: name of file to which the index is written
.. code:: python .. code:: python
map(query_seq) map(query_seq)
This methods maps `query_seq` against the index. It *yields* a generator, This methods maps :code:`query_seq` against the index. It *yields* a generator,
generating a series of `Alignment` objects. generating a series of :code:`Alignment` objects.
Class minimap2.Alignment Class minimap2.Alignment
~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~
This class has the following properties: This class has the following properties:
* `ctg`: name of the reference sequence the query is mapped to * **ctg**: name of the reference sequence the query is mapped to
* `ctg_len`: total length of the reference sequence * **ctg_len**: total length of the reference sequence
* `r_st` and `r_en`: start and end positions on the reference * **r_st** and **r_en**: start and end positions on the reference
* `q_st` and `q_en`: start and end positions on the query * **q_st** and **q_en**: start and end positions on the query
* `strand`: +1 if on the forward strand; -1 if on the reverse strand * **strand**: +1 if on the forward strand; -1 if on the reverse strand
* `mapq`: mapping quality * **mapq**: mapping quality
* `NM`: number of mismatches and gaps in the alignment * **NM**: number of mismatches and gaps in the alignment
* `blen`: length of the alignment, including both alignment matches and gaps * **blen**: length of the alignment, including both alignment matches and gaps
* `trans_strand`: transcript strand. +1 if on the forward strand; -1 if on the * **trans_strand**: transcript strand. +1 if on the forward strand; -1 if on the
reverse strand; 0 if unknown reverse strand; 0 if unknown
* `is_primary`: if the alignment is primary (typically the best and the first * **is_primary**: if the alignment is primary (typically the best and the first
to generate) to generate)
* `cigar_str`: CIGAR string * **cigar_str**: CIGAR string
* `cigar`: CIGAR returned as an array of shape `(n_cigar,2)`. The two numbers * **cigar**: CIGAR returned as an array of shape :code:`(n_cigar,2)`. The two
give the length and the operator of each CIGAR operation. numbers give the length and the operator of each CIGAR operation.
An Alignment object can be converted to a string in the following format: An Alignment object can be converted to a string in the following format: