windowmasker reads from a file called `-` instead of from `stdin`.

[charles-plessy]

Dear BLAST developers,

I would like to pass input to windowmasker through stdin so that I can transparently support compressed inputs, with zcat -f.

However, windowmasker does not appear to read from stdin. Instead, it it searches for a file called -.

$ printf '>test\nAAA\n' > test.fa
$ cat test.fa | windowmasker -mk_counts -genome_size 3
Info: (106.11) Registry file of application "windowmasker" is not found
pass 1
Error: (CIOException::eRead) Read error
Error: (106.16) Application's execution failed (CIOException::eRead) Read error

$ printf '>test\nAAA\n' > -
$ windowmasker -mk_counts -genome_size 3
Info: (106.11) Registry file of application "windowmasker" is not found
pass 1
pass 2
##windowmasker-statistics-format-version:ascii 1.0.0
##windowmasker-statistics-algorithm-version:1.0.0
##parameters:unit=1 t_low=3 t_high=3
1
0 3
[etc]

Can you fix windowmasker to read on stdin ?

Best regards,

Charles Plessy

[ucko]

Hi, Charles.

I have passed this report on to windowmasker's developer; meanwhile, AFAICT, you can explicitly supply -in /dev/stdin.