#43 reformat.sh extin flag not working for bash process substitutions

[Andrew Schriefer]

Hello,

The reformat.sh extin flag is not working properly for bash process substitutions. I am using version BBMap version 38.87 on linux. I run this command on the attached fastq file:

reformat.sh extin=.fa minlength=36 out=stdout.fa in=<(reformat.sh int=f in=test_R1.fq.gz out=stdout.fa ftl=17)

And I get this error "Warning: Did not find expected fasta file extension for filename /dev/fd/63":

Set INTERLEAVED to false
Input is being processed as unpaired
Input: 2 reads 502 bases
Warning: Did not find expected fasta file extension for filename /dev/fd/63
Input is being processed as unpaired
FTrimmed: 2 reads (100.00%) 34 bases (6.77%)
Output: 2 reads (100.00%) 468 bases (93.23%)

Time: 0.157 seconds.
Reads Processed: 2 0.01k reads/sec
Bases Processed: 502 0.00m bases/sec
Input: 0 reads 0 bases
Short Read Discards: 0 reads (NaN%) 0 bases (NaN%)
Output: 0 reads (NaN%) 0 bases (NaN%)

Time: 0.195 seconds.
Reads Processed: 0 0.00k reads/sec
Bases Processed: 0 0.00m bases/sec