viral_seq 1.2.7 → 1.2.8

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data/README.md CHANGED
@@ -179,10 +179,14 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
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  ## Updates
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+ ### Version 1.2.8-07292021
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+
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+ 1. Fixed an issue when reading .fastq files containing blank_lines.
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+
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  ### Version 1.2.7-07152021
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- 1. Optimzed the workflow of the `tcs` pipeline on raw data with uneven lengths.
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- `tcs` version to v2.3.5.
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+ 1. Optimzed the workflow of the `tcs` pipeline on raw data with uneven lengths.
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+ `tcs` version to v2.3.6.
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  ### Version 1.2.6-07122021
@@ -116,6 +116,8 @@ module ViralSeq
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  File.open(fastq_file,'r') do |file|
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  file.readlines.collect do |line|
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+ line.tr!("\u0000","")
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+ next if line == "\n"
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  count +=1
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  count_m = count % 4
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  if count_m == 1
@@ -305,7 +305,8 @@ module ViralSeq
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  end
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  def general_filter(seq)
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- if seq.size < ($platform_sequencing_length - 1)
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+ return false unless seq
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+ if seq.size < ($platform_sequencing_length - 10)
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  return false
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  elsif seq[1..-2] =~ /N/ # sequences with ambiguities except the 1st and last position removed
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  return false
@@ -2,6 +2,6 @@
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  # version info and histroy
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  module ViralSeq
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- VERSION = "1.2.7"
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- TCS_VERSION = "2.3.6"
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+ VERSION = "1.2.8"
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+ TCS_VERSION = "2.3.7"
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: viral_seq
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  version: !ruby/object:Gem::Version
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- version: 1.2.7
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+ version: 1.2.8
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  platform: ruby
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  authors:
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  - Shuntai Zhou
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2021-07-15 00:00:00.000000000 Z
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+ date: 2021-07-30 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bundler