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Update snap.rb to fix failure to build index #252

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Update snap.rb to fix failure to build index #252

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a390b68
Update snap.rb to fix failure to build index
IdoBar Mar 20, 2024
ca05de6
Update snap.rb to handle deleting of non-empty index folders
IdoBar Mar 22, 2024
74b0850
Merge pull request #1 from IdoBar/IdoBar-patch-2
IdoBar Mar 22, 2024
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5 changes: 3 additions & 2 deletions lib/transrate/snap.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ class SnapError < TransrateError
class Snap

require 'bio'
require 'fileutils'

attr_reader :index_name, :bam, :read_count

Expand Down Expand Up @@ -138,10 +139,10 @@ def build_index file, threads
runner.run
if !runner.status.success?
err = runner.stderr
if err =~ /Ran out of overflow table namespace/ || err =~ /Trying to use too many overflow entries/
if err =~ /Ran out of overflow table namespace/ || err =~ /Trying to use too many overflow entries/ || err =~ /Genome is too big for 4 byte genome locations/
logger.warn "Snap index build failed with n = #{n} , increasing +1"
n += 1
Dir.delete(@index_name) if Dir.exist?(@index_name)
FileUtils.rm_rf(@index_name) if Dir.exist?(@index_name)
else
msg = "Failed to build Snap index\n#{runner.stderr}"
raise SnapError.new(msg)
Expand Down