viral_seq 1.2.1 → 1.2.2

checksums.yaml

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

@@ -31,7 +31,7 @@ Specifically for Primer ID sequencing and HIV drug resistance analysis.
 ### Excutables
 
 ### `tcs`  
-Use executable `tcs` pipeline to process **Primer ID MiSeq sequencing** data.
+Use executable `tcs` pipeline (v2.3.2) to process **Primer ID MiSeq sequencing** data.
 
 Example commands:
 ```bash
@@ -175,6 +175,11 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
+### Version 1.2.2-05272021
+
+  1. Fixed a bug in the `tcs` pipeline that sometimes causes `SystemStackError`.
+  `tcs` pipeline upgraded to v2.3.2
+
 ### Version 1.2.1-05172021
 
   1. Added a function in R to check and install missing R packages for `tcs_sdrm` pipeline.

data/bin/tcs

@@ -371,9 +371,21 @@ primers.each do |primer|
   # Primer ID distribution in .json file
   out_pid_json = File.join(out_dir_set, 'primer_id.json')
   pid_json = {}
-  pid_json[:primer_id_in_use] = Hash[*(primer_id_in_use.sort_by {|k, v| [-v,k]}.flatten)]
-  pid_json[:primer_id_distribution] = Hash[*(primer_id_dis.sort_by{|k,v| k}.flatten)]
-  pid_json[:primer_id_frequency] = Hash[*(primer_id_count.sort_by {|k, v| [-v,k]}.flatten)]
+  pid_json[:primer_id_in_use] = {}
+  primer_id_in_use.sort_by {|k, v| [-v,k]}.each do |k,v|
+    pid_json[:primer_id_in_use][k] = v
+  end
+
+  pid_json[:primer_id_distribution] = {}
+  primer_id_dis.sort_by{|k,v| k}.each do |k,v|
+    pid_json[:primer_id_distribution][k] = v
+  end
+
+  pid_json[:primer_id_frequency] = {}
+  primer_id_count.sort_by {|k,v| [-v,k]}.each do |k,v|
+    pid_json[:primer_id_frequency][k] = v
+  end
+
   File.open(out_pid_json, 'w') do |f|
     f.puts JSON.pretty_generate(pid_json)
   end
@@ -490,6 +502,6 @@ unless options[:keep]
   File.unlink(r1_f)
   File.unlink(r2_f)
 end
-log.puts Time.now.to_s + "\t" + "TCS pipeline successfuly exercuted."
+log.puts Time.now.to_s + "\t" + "TCS pipeline successfuly executed."
 log.close
 puts "DONE!"

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.2.1"
-  TCS_VERSION = "2.3.1"
+  VERSION = "1.2.2"
+  TCS_VERSION = "2.3.2"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.2.1
+  version: 1.2.2
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-05-17 00:00:00.000000000 Z
+date: 2021-05-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler