ready to stage files

src/curation_tool.cr

@@ -1,5 +1,3 @@
-#!/bin/env crystal
-
 require "option_parser"
 require "./lib/curation_tool"
 
@@ -19,7 +17,7 @@ OptionParser.parse do |parser|
   parser.on("-w", "--setup_working_dir", "create initial curation files and directory") { tol = true }
   parser.on("-r", "--build_release", "create pretext and release files") { release = true }
   parser.on("-q", "--copy_qc", "copy from DIR to curation for QC") { qc = true }
-  parser.on("-m", "--merged", "build files based on a merged map") {merged = true}
+  parser.on("-m", "--merged", "build files based on a merged map") { merged = true }
   parser.on("-g", "--highres", "build a highres pretext") { highres = true }
 
   parser.on("-h", "--help", "show this help") do
@@ -40,7 +38,7 @@ OptionParser.parse do |parser|
   end
 end
 
-y = GritJiraIssue.new(issue,merged)
+y = GritJiraIssue.new(issue, merged)
 
 # puts y.json.to_pretty_json
 

src/get_assc_stats.cr

@@ -71,7 +71,7 @@ puts ["tolID", "fasta file", "average gc", "average length", "average repeat", "
       "false negatives", "average gc fn", "average len fn", "average repeat fn", "average stops dn"].join("\t")
 
 ARGV.each { |jira_id|
-  y = StatIssue.new(jira_id)
+  y = StatIssue.new(jira_id, false)
 
   Dir.glob("#{y.decon_dir}/*.contamination").each { |file|
     contamination_ids = parse_decon_file(file)

src/lib/curation_tool.cr

@@ -11,7 +11,9 @@ module CurationTool
     fasta_gz = y.decon_file.sub(/contamination.*/, "decontaminated.fa.gz")
 
     if y.merged
-      fasta_gz = # largestdna.ref in the assembly/draft/treeval directory
+      # largest dna.ref in the assembly/draft/treeval directory
+      treeval_dir = y.decon_file.sub(/draft.*/, "/draft/treeval/")
+      fasta_gz = Dir["#{treeval_dir}/*/data/ref.fa"].sort_by { |file| File.info(file).size }[-1]
     end
 
     raise Exception.new("scaffolds.tpf in working #{wd} already exists") if File.exists?(wd + "/scaffolds.tpf")

src/lib/grit_jira_issue.cr

@@ -1,5 +1,3 @@
-#!/bin/env crystal
-
 require "http/client"
 require "html"
 require "json"
@@ -9,12 +7,12 @@ require "file_utils"
 class GritJiraIssue
   @@url = "jira.sanger.ac.uk"
   @token : String?
-  property merged : Bool
 
-  def initialize(name : String, merged : Bool)
+  getter merged
+
+  def initialize(name : String, @merged : Bool = false)
     @id = name
     @token = self.get_token
-    @merged = merged
   end
 
   def json
@@ -60,14 +58,11 @@ class GritJiraIssue
   # in the form of tol_id _ version
   def sample_version
     "#{self.tol_id}_#{self.release_version}"
-<<<<<<< HEAD:src/lib/GritJiraIssue.cr
-=======
   end
 
   # in the form of tol_id . version
   def sample_dot_version
     "#{self.tol_id}.#{self.release_version}"
->>>>>>> main:src/lib/grit_jira_issue.cr
   end
 
   # curation working directory

src/submit_btk.cr

@@ -67,5 +67,5 @@ __HERE__
   end
 end
 
-y = BTKIssue.new(issue)
+y = BTKIssue.new(issue, false)
 y.submit_to_lsf

src/submit_fcs.cr

@@ -48,6 +48,6 @@ OptionParser.parse do |parser|
 end
 
 issues.each { |issue|
-  y = FCSIssue.new(issue)
+  y = FCSIssue.new(issue, false)
   y.submit_to_lsf
 }