viral_seq 1.10.0 → 1.10.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -11,3 +11,5 @@
 
 # gem files
 *.gem
+
+.DS_Store

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    viral_seq (1.10.1)
+    viral_seq (1.10.0)
       colorize (~> 0.1)
       combine_pdf (~> 1.0, >= 1.0.0)
       muscle_bio (= 0.4)

data/README.md

@@ -191,7 +191,11 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
-### Version-1.10.1
+### Version-1.10.2-07210225
+
+1. Fixed a bug processing parameters for HIV sequence QC.
+
+### Version-1.10.1-05012025
 
 1. Added quality filter for Illumina 2-color sequencing platforms (filter poly-G and poly-C)
 2. Replaced `MuscleBio` with [`VirustLocator`]("https://github.com/ViralSeq/virust-locator-ruby") for faster and more accurate pairwise alignment.

data/lib/viral_seq/seq_hash.rb

@@ -1440,8 +1440,10 @@ module ViralSeq
     def position_helper(position)
       if position.is_a?(Range)
         return position
-      elsif position.is_a?(Integer)
+      elsif position.is_a?(Integer) && position > 0
         return position..position
+      elsif position.is_a?(Integer) && position == 0
+        return 0..1000000
       elsif position.is_a?(String)
         return position.to_i..position.to_i
       elsif position.is_a?(Array)

data/lib/viral_seq/tcs_dr.rb

@@ -65,7 +65,7 @@ module ViralSeq
          :TCS_QC=>true,
          :ref_genome=>"HXB2",
          :ref_start=>6585,
-         :ref_end=>7205..7210,
+         :ref_end=>7208,
          :indel=>true,
          :trim=>false},
          {:region=>"CA",
@@ -146,7 +146,7 @@ module ViralSeq
         :TCS_QC=>true,
         :ref_genome=>"HXB2",
         :ref_start=>6585,
-        :ref_end=>7205..7210,
+        :ref_end=>7208,
         :indel=>true,
         :trim=>false},
         {:region=>"CA",
@@ -226,7 +226,7 @@ module ViralSeq
         :TCS_QC=>true,
         :ref_genome=>"HXB2",
         :ref_start=>6585,
-        :ref_end=>7205..7210,
+        :ref_end=>7208,
         :indel=>true,
         :trim=>false},
         {:region=>"CA",
@@ -307,7 +307,7 @@ module ViralSeq
         :TCS_QC=>true,
         :ref_genome=>"HXB2",
         :ref_start=>6585,
-        :ref_end=>7205..7210,
+        :ref_end=>7208,
         :indel=>true,
         :trim=>false},
         {:region=>"CA",

data/lib/viral_seq/tcs_json.rb

@@ -101,10 +101,10 @@ module ViralSeq
 
               data[:ref_genome] = get_ref
 
-              print "reference 5'end ref position or posiiton range, 0 if no need to match this end \n> "
+              print "reference 5'end ref position or position range, 0 if no need to match this end \n> "
               data[:ref_start] = gets.chomp.rstrip.to_i
 
-              print "reference 3'end ref position or posiiton range: 0 if no need to match this end \n> "
+              print "reference 3'end ref position or position range: 0 if no need to match this end \n> "
               data[:ref_end] = gets.chomp.rstrip.to_i
 
               print "allow indels? (default as yes) Y/N \n> "

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.10.0"
-  TCS_VERSION = "2.7.2"
+  VERSION = "1.10.2"
+  TCS_VERSION = "2.7.3"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.10.0
+  version: 1.10.2
 platform: ruby
 authors:
 - Shuntai Zhou