Chastity filter and flags
I'm having the same issue with currently latest version (38.90).
Just discovered the extin=fq parameter. But having reformat.sh in1=<(preprocess "$fq1") in2=<(preprocess "$fq2") extin=fq qin=33 ... does not solve the issue either: $ reformat.sh qin=33 extin=fq in1=<(<test_1.fastq) in2=<(<test_2.fastq) out=test.sam java -ea -Xms300m -cp /apps/BBMAP/38.57/bbmap/current/ jgi.ReformatReads qin=33 extin=fq in1=/dev/fd/63 in2=/dev/fd/62 out=test.sam Executing jgi.ReformatReads [qin=33, extin=fq, in1=/dev/fd/63, in2=/dev/fd/62, out=test.sam] Set INTERLEAVED to false...
Just discovered the extin=fq parameter. But having reformat.sh in1=<(preprocess "$fq1").fq in2=<(preprocess "$fq2").fq extin=fq qin=33 ... does not solve the issue either: $ reformat.sh qin=33 extin=fq in1=<(<test_1.fastq) in2=<(<test_2.fastq) out=test.sam java -ea -Xms300m -cp /apps/BBMAP/38.57/bbmap/current/ jgi.ReformatReads qin=33 extin=fq in1=/dev/fd/63 in2=/dev/fd/62 out=test.sam Executing jgi.ReformatReads [qin=33, extin=fq, in1=/dev/fd/63, in2=/dev/fd/62, out=test.sam] Set INTERLEAVED to...
Multiple streams input