temp files not created in tempdefault

[rec3141]

after setting set.dir(tempdefault=/tmp) I would expect temporary files to be created in /tmp, but e.g. make.contigs and count.seqs still create .temp and .num.temp files in the mothur executable directory using mothur v.1.39.5.

[mothur-westcott]

Thanks for bringing this to our attention. We will add it to the list.

[mothur-westcott]

• Add scratch parameter to set.dir to set location of temp files
• Find all places in source mothur creates files and adjust locations

[mothur-westcott]

Instead of scratch, all files will be created in the outputdir.
If this outputdir not set, output files are created in the location of the input file.