hisat2 hangs on bad options when stdout is piped

[knightjimr]

When I run the following command (note the incorrect underscore in "--summary_file"), I get the appropriate error message and the program stops:

hisat2 -x $REF -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz --summary_file xxx.txt

(where $REF is the path to the reference, and the reference and read files are valid files).

However, when I add piping of stdout to samtools, as in this command, I get the error message, but hisat2 then hangs until I kill it:

hisat2 -x $REF -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz --summary_file xxx.txt | samtools view -hbS - > align.bam

This is with release 2.1.0.

[parkchanhee]

https://github.com/infphilo/hisat2/commit/47c5f9a5c9a83bf83a95aa60e622980e0837b4af

[parkchanhee]

Fixed - it's available in the master branch.