There should be a way to view the logs that bwa emits

[clintval]

Interaction with BWA is implemented using ExecutableRunner.

By default, all IO channels are set to PIPE:

prymer/prymer/util/executable_runner.py

Lines 42 to 44 in 70f6840

	stdin: int = subprocess.PIPE,
	stdout: int = subprocess.PIPE,
	stderr: int = subprocess.PIPE,

BWA doesn't override any of them.

prymer/prymer/offtarget/bwa.py

Line 285 in 70f6840

super().__init__(command=command)

To interact with the PIPEs BWA will read and write to the private subprocess:

prymer/prymer/offtarget/bwa.py

Line 296 in 70f6840

self._subprocess.stdin.write(fastq_str)

prymer/prymer/offtarget/bwa.py

Line 298 in 70f6840

self._reader = sam.reader(path=self._subprocess.stdout, file_type=sam.SamFileType.SAM)

I think there is a small memory use bug here in that stderr will be written to a pipe that will never be read from. A buffer may be created and only increase in size. Regardless, I think that stderr should be redirected to a logging stream (perhaps with DEBUG level) so that a user has a way of reading them.

Originally raised in: #32 (comment)

[clintval]

Sister issue for Primer3:

• Error messages are not always propagated through primer3_error #15