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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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working with fa files #84

Closed jordi-vaquero closed 4 years ago

jordi-vaquero commented 5 years ago

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

timbitz commented 5 years ago

Whippet does not work with FASTA only FASTQ-- its alignment algorithm utilizes the quality scores.