viral_seq 1.2.7 → 1.2.8

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data/README.md

@@ -179,10 +179,14 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
 
 ## Updates
 
+### Version 1.2.8-07292021
+
+  1. Fixed an issue when reading .fastq files containing blank_lines.
+
 ### Version 1.2.7-07152021
 
-  1. Optimzed the workflow of the `tcs` pipeline on raw data with uneven lengths. 
-  `tcs` version to v2.3.5.
+  1. Optimzed the workflow of the `tcs` pipeline on raw data with uneven lengths.
+  `tcs` version to v2.3.6.
 
 
 ### Version 1.2.6-07122021

data/lib/viral_seq/seq_hash.rb

@@ -116,6 +116,8 @@ module ViralSeq
 
       File.open(fastq_file,'r') do |file|
         file.readlines.collect do |line|
+          line.tr!("\u0000","")
+          next if line == "\n"
           count +=1
           count_m = count % 4
           if count_m == 1

data/lib/viral_seq/tcs_core.rb

@@ -305,7 +305,8 @@ module ViralSeq
       end
 
       def general_filter(seq)
-        if seq.size < ($platform_sequencing_length - 1)
+        return false unless seq
+        if seq.size < ($platform_sequencing_length - 10)
           return false
         elsif seq[1..-2] =~ /N/ # sequences with ambiguities except the 1st and last position removed
           return false

data/lib/viral_seq/version.rb

@@ -2,6 +2,6 @@
 # version info and histroy
 
 module ViralSeq
-  VERSION = "1.2.7"
-  TCS_VERSION = "2.3.6"
+  VERSION = "1.2.8"
+  TCS_VERSION = "2.3.7"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: viral_seq
 version: !ruby/object:Gem::Version
-  version: 1.2.7
+  version: 1.2.8
 platform: ruby
 authors:
 - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-07-15 00:00:00.000000000 Z
+date: 2021-07-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler