From 7da9a08a6fa12d72808be622cbf48b8ab9d39acb Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 16 Sep 2017 22:36:19 -0400 Subject: [PATCH] reformat --- python/README.rst | 58 +++++++++++++++++++++++------------------------ 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/python/README.rst b/python/README.rst index fb48393..173a03c 100644 --- a/python/README.rst +++ b/python/README.rst @@ -52,71 +52,71 @@ Class minimap2.Aligner 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 sequence file can be optionally gzip'd. -* `preset`: minimap2 preset. Currently, minimap2 supports the following - presets: `sr` for single-end short reads; `map-pb` for PacBio - read-to-reference mapping; `map-ont` for Oxford Nanopore read mapping; - `splice` for long-read spliced alignment; `asm5` for assembly-to-assembly - alignment; `asm10` for full genome alignment of closely related species. Note +* **preset**: minimap2 preset. Currently, minimap2 supports the following + presets: **sr** for single-end short reads; **map-pb** for PacBio + read-to-reference mapping; **map-ont** for Oxford Nanopore read mapping; + **splice** for long-read spliced alignment; **asm5** for assembly-to-assembly + alignment; **asm10** for full genome alignment of closely related species. Note 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 map(query_seq) -This methods maps `query_seq` against the index. It *yields* a generator, -generating a series of `Alignment` objects. +This methods maps :code:`query_seq` against the index. It *yields* a generator, +generating a series of :code:`Alignment` objects. Class minimap2.Alignment ~~~~~~~~~~~~~~~~~~~~~~~~ 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 -* `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) -* `cigar_str`: CIGAR string +* **cigar_str**: CIGAR string -* `cigar`: CIGAR returned as an array of shape `(n_cigar,2)`. The two numbers - give the length and the operator of each CIGAR operation. +* **cigar**: CIGAR returned as an array of shape :code:`(n_cigar,2)`. The two + numbers give the length and the operator of each CIGAR operation. An Alignment object can be converted to a string in the following format: