minimap2 0.0.3 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -35,14 +35,23 @@ Ruby-minimap2 is tested on Ubuntu and macOS.
 
 ```ruby
 require "minimap2"
+```
+
+create aligner
 
-# load or build index
+```ruby
 aligner = Minimap2::Aligner.new("minimap2/test/MT-human.fa")
+```
+
+retrieve a subsequence from the index
 
-# retrieve a subsequence from the index
+```ruby
 seq = aligner.seq("MT_human", 100, 200)
+```
 
-# mapping
+mapping
+
+```ruby
 hits = aligner.align(seq)
 pp hits[0].to_h
 # {:ctg          => "MT_human",

data/lib/minimap2/ffi/constants.rb

@@ -77,6 +77,7 @@ module Minimap2
         :sdust_thres,          :int,     # score threshold for SDUST; 0 to disable
         :max_qlen,             :int,     # max query length
         :bw,                   :int,     # bandwidth
+        :bw_long,              :int,
         :max_gap,              :int,     # break a chain if there are no minimizers in a max_gap window
         :max_gap_ref,          :int,
         :max_frag_len,         :int,
@@ -85,14 +86,14 @@ module Minimap2
         :min_cnt,              :int,     # min number of minimizers on each chain
         :min_chain_score,      :int,     # min chaining score
         :chain_gap_scale,      :float,
+        :rmq_size_cap,         :int,
+        :rmq_inner_dist,       :int,
+        :rmq_rescue_size,      :int,
+        :rmq_rescue_ratio,     :float,
         :mask_level,           :float,
         :mask_len,             :int,
         :pri_ratio,            :float,
         :best_n,               :int,     # top best_n chains are subjected to DP alignment
-        :max_join_long,        :int,
-        :max_join_short,       :int,
-        :min_join_flank_sc,    :int,
-        :min_join_flank_ratio, :float,
         :alt_drop,             :float,
         :a,                    :int,     # matching score
         :b,                    :int,     # mismatch

data/lib/minimap2/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Minimap2
-  VERSION = '0.0.3'
+  VERSION = '0.0.4'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-01 00:00:00.000000000 Z
+date: 2021-05-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -131,7 +131,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.3
+rubygems_version: 3.2.15
 signing_key: 
 specification_version: 4
 summary: minimap2