cagnut_bwa 0.3.2 → 0.3.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 97a5d23cc8316d1b59b094e87e31d8ee1aac2308
-  data.tar.gz: 0b79d3b340ddb09a6c0d685e70d4f0a679cffecf
+  metadata.gz: 2e4b4f7800e674673c6c89535427a3338b1be1e4
+  data.tar.gz: b01d2b22d2987f7bd637338cba42cac186b04200
 SHA512:
-  metadata.gz: ec0ef694d43675ba5e27548d63ab818e0fe57c1b574ffae58648a19da42fe84266fb2d0222ada1437c9f7b5ee59cac680e2ba4bde5c84cd4c96b4164cf28157e
-  data.tar.gz: c36780081df3e223280c5ac07c917432df5b131f955cd5885d2c82a575850cafe7d2c0eb609b086158f18b5154f5a4d4df0a6b88f2c160998255e403e0071dda
+  metadata.gz: 4f4b424a1418f8a142723ba283d0fae36eee7e2f56354e50b7a3a6610982dd15ee4770304fe852a39686e0c95eb927ec8b0aed7d97031fff8c5e7f1f0be4d0d8
+  data.tar.gz: ed764a78b7f6e845908ec97bd39134c59ac37a2de02ac3d087fe8acb6f2ab6fa8ac93ee31b3ab287fa23bd90284335919cc622f548efb3418950dac7a4fa26b3

data/lib/cagnut_bwa/check_tools.rb

@@ -3,7 +3,7 @@ module CagnutBwa
     def check_tool tools_path, refs=nil
       super if defined?(super)
       ver = check_bwa tools_path['bwa'], refs['ref_fasta']
-      check_bwa_index tools_path['bwa'], refs['ref_fasta'] if ver.blank?
+      check_bwa_index tools_path['bwa'], refs['ref_fasta'] if !ver.blank?
     end
 
     def check_bwa path, ref_path

data/lib/cagnut_bwa/functions/templates/aln.sh

@@ -26,14 +26,14 @@ else
 fi
 
 #check for correct number of sequences processed, based on fastq records
-PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
 
 echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
 echo "bwa processed" $PROCESSED
 
 if [[ "#{input}" =~ gz$ ]]
 then
-  LINESFASTQ1=$(zcat "#{input}" | wc -l)
+  LINESFASTQ1=$(gunzip -c "#{input}" | wc -l)
 else
 # non gz files
   LINESFASTQ1=$(wc -l "#{input}" | cut -d" " -f1 )
@@ -79,13 +79,13 @@ else
 fi
 
 #check for correct number of sequences processed, based on fastq records
-PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
 echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
 echo "bwa processed" $PROCESSED
 
 if [[ "#{input2}" =~ gz$ ]]
 then
-  LINESFASTQ2=$(zcat "#{input2}" | wc -l)
+  LINESFASTQ2=$(gunzip -c "#{input2}" | wc -l)
 else
 # non gz files
   LINESFASTQ2=$(wc -l "#{input2}" | cut -d" " -f1 )

data/lib/cagnut_bwa/functions/templates/bwa_samp_one_fastq.sh

@@ -26,7 +26,7 @@ else
 fi
 
 #check for correct number of sequences processed, based on fastq records
-PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
 
 echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
 echo "bwa processed" $PROCESSED
@@ -34,8 +34,8 @@ echo "bwa processed" $PROCESSED
 if [[ "#{seq}" =~ gz$ ]]
 then
 
-  LINESFASTQ1=$(zcat "#{seq}" | wc -l)
-  LINESFASTQ2=$(zcat "#{seq2}" | wc -l)
+  LINESFASTQ1=$(gunzip -c "#{seq}" | wc -l)
+  LINESFASTQ2=$(gunzip -c "#{seq2}" | wc -l)
 
 else
 # non gz files

data/lib/cagnut_bwa/functions/templates/bwa_samse_one_fastq.sh

@@ -27,7 +27,7 @@ fi
 
 #check for correct number of sequences processed, based on fastq records
 
-PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
 
 echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
 echo "bwa processed" $PROCESSED

data/lib/cagnut_bwa/functions/templates/samp.sh

@@ -35,15 +35,15 @@ else
 fi
 
 #check for correct number of sequences processed, based on fastq records
-PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o -P " \\d+ ")
+PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep " sequences have been processed." | grep -o "[0-9]\+")
 
 echo "checking stdout file: " #{jobs_dir}/#{script_name}.err
 echo "bwa processed" $PROCESSED
 
 if [[ "#{fastq}" =~ gz$ ]]
 then
-  LINESFASTQ1=$(zcat "#{fastq}" | wc -l)
-  LINESFASTQ2=$(zcat "#{fastq2}.gz" | wc -l)
+  LINESFASTQ1=$(gunzip -c "#{fastq}" | wc -l)
+  LINESFASTQ2=$(gunzip -c "#{fastq2}" | wc -l)
 else
 # non gz files
   LINESFASTQ1=$(wc -l "#{fastq}" | cut -d" " -f1 )

data/lib/cagnut_bwa/version.rb

@@ -1,3 +1,3 @@
 module CagnutBwa
-  VERSION = "0.3.2"
+  VERSION = "0.3.3"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cagnut_bwa
 version: !ruby/object:Gem::Version
-  version: 0.3.2
+  version: 0.3.3
 platform: ruby
 authors:
 - Shi-Gang Wang
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-11-07 00:00:00.000000000 Z
+date: 2016-11-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cagnut_core