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cihga39871 / Atria

An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.
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ERROR: UndefVarError: uncompressed_size1 not defined on gzipped single-end input #2

Closed genec1 closed 2 years ago

genec1 commented 2 years ago

Running atria on gzipped single-end input gives me this error: ERROR: UndefVarError: uncompressed_size1 not defined 

Stacktrace:
 [1] (::Atria.Trimmer.var"#cycle_wrapper_single_end#31"{Array{UInt8,1},Int64,NTuple{60,Array{Atria.FqRecords.FqRecord,1}},Array{Bool,1},Array{Array{UInt8,1},1}})() at /home/jc/projects/atria/src/Trimmer/wrapper_single_end.jl:421
 [2] julia_wrapper_atria_single_end(::Array{String,1}; exit_after_help::Bool) at /home/jc/projects/atria/src/Trimmer/wrapper_single_end.jl:464
 [3] julia_wrapper_atria_single_end at /home/jc/projects/atria/src/Trimmer/wrapper_single_end.jl:6 [inlined]
 [4] julia_main() at /home/jc/projects/atria/src/Atria.jl:74
 [5] top-level scope at none:1

Looking at the location of the error (Trimmer/wrapper_single_end.jl:421), it appears to be the first use of uncompressed_size1 in that file. The only place where I see uncompressed_size1 being defined is by the chunk_sizes function in Trimmer/wrapper.jl which works on two input files, not one.

cihga39871 commented 2 years ago

Thank you for supporting Atria. It is fixed in the master branch (v3.0.2).