Is whippet working with fa files instead of fastq? I have a set of files that doesn't contain quality string, and the following error appears
[1] _read!(::BioSequences.FASTQ.Reader, ::BioCore.Ragel.State{BufferedStreams.BufferedInputStream{BufferedStreams.BufferedInputStream{Libz.Source{:inflate,BufferedStreams.BufferedInputStream{IOStream}}}}}, ::BioSequences.FASTQ.Record) at /home/jordi/.julia/v0.6/BioCore/src/ReaderHelper.jl:164[2] read! at /home/jordi/.julia/v0.6/BioCore/src/ReaderHelper.jl:134 [inlined][3] read! at /home/jordi/.julia/v0.6/Whippet/src/record.jl:11 [inlined][4] read_chunk! at /home/jordi/.julia/v0.6/Whippet/src/reads.jl:17 [inlined][5] #process_paired_reads!#62(::Int64, ::Bool, ::Int64, ::Requests.ResponseStream{TCPSocket}, ::Requests.ResponseStream{TCPSocket}, ::Bool, ::Function, ::BioSequences.FASTQ.Reader, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.DefaultBiasMod) at /home/jordi/.julia/v0.6/Whippet/src/reads.jl:151[6] (::Whippet.#kw##process_paired_reads!)(::Array{Any,1}, ::Whippet.#process_paired_reads!, ::BioSequences.FASTQ.Reader, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.DefaultBiasMod) at ./<missing>:0[7] macro expansion at /home/jordi/.julia/v0.6/Whippet/src/timer.jl:5 [inlined][8] main() at /home/jordi/.julia/v0.6/Whippet/bin/whippet-quant.jl:169[9] include_from_node1(::String) at ./loading.jl:576[10] include(::String) at ./sysimg.jl:14[11] process_options(::Base.JLOptions) at ./client.jl:305[12] _start() at ./client.jl:371while loading /home/jordi/.julia/v0.6/Whippet/bin/whippet-quant.jl, in expression starting on line 5
Is whippet working with fa files instead of fastq? I have a set of files that doesn't contain quality string, and the following error appears
[1] _read!(::BioSequences.FASTQ.Reader, ::BioCore.Ragel.State{BufferedStreams.BufferedInputStream{BufferedStreams.BufferedInputStream{Libz.Source{:inflate,BufferedStreams.BufferedInputStream{IOStream}}}}}, ::BioSequences.FASTQ.Record) at /home/jordi/.julia/v0.6/BioCore/src/ReaderHelper.jl:164
[2] read! at /home/jordi/.julia/v0.6/BioCore/src/ReaderHelper.jl:134 [inlined]
[3] read! at /home/jordi/.julia/v0.6/Whippet/src/record.jl:11 [inlined]
[4] read_chunk! at /home/jordi/.julia/v0.6/Whippet/src/reads.jl:17 [inlined]
[5] #process_paired_reads!#62(::Int64, ::Bool, ::Int64, ::Requests.ResponseStream{TCPSocket}, ::Requests.ResponseStream{TCPSocket}, ::Bool, ::Function, ::BioSequences.FASTQ.Reader, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.DefaultBiasMod) at /home/jordi/.julia/v0.6/Whippet/src/reads.jl:151
[6] (::Whippet.#kw##process_paired_reads!)(::Array{Any,1}, ::Whippet.#process_paired_reads!, ::BioSequences.FASTQ.Reader, ::BioSequences.FASTQ.Reader, ::Whippet.AlignParam, ::Whippet.GraphLib, ::Whippet.GraphLibQuant{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.MultiMapping{Whippet.SGAlignPaired,Whippet.DefaultCounter}, ::Whippet.DefaultBiasMod) at ./<missing>:0
[7] macro expansion at /home/jordi/.julia/v0.6/Whippet/src/timer.jl:5 [inlined]
[8] main() at /home/jordi/.julia/v0.6/Whippet/bin/whippet-quant.jl:169
[9] include_from_node1(::String) at ./loading.jl:576
[10] include(::String) at ./sysimg.jl:14
[11] process_options(::Base.JLOptions) at ./client.jl:305
[12] _start() at ./client.jl:371
while loading /home/jordi/.julia/v0.6/Whippet/bin/whippet-quant.jl, in expression starting on line 5