Closed peterjc closed 3 months ago
Something is broken indeed:
(xopen) rhpvorderman@tuxminator:~/PycharmProjects/xopen$ pip list | grep xopen
xopen 2.0.0
(xopen) rhpvorderman@tuxminator:~/PycharmProjects/xopen$ wc -l ~/test/5millionreads_R1.fastq
20000000 /home/rhpvorderman/test/5millionreads_R1.fastq
(xopen) rhpvorderman@tuxminator:~/PycharmProjects/xopen$ cat ~/test/5millionreads_R1.fastq | python -c 'import xopen; f=xopen.xopen("/dev/stdin", "rt"); print(f.read())' | wc -l
19999956
(xopen) rhpvorderman@tuxminator:~/PycharmProjects/xopen$ cat ~/test/5millionreads_R1.fastq | python -c 'import xopen; f=xopen.xopen("-", "rt"); print(f.read())' | wc -l
19999956
(xopen) rhpvorderman@tuxminator:~/PycharmProjects/xopen$ pip install xopen==1.9.0 >/dev/null
(xopen) rhpvorderman@tuxminator:~/PycharmProjects/xopen$ cat ~/test/5millionreads_R1.fastq | python -c 'import xopen; f=xopen.xopen("-", "rt"); print(f.read())' | wc -l
20000001
(xopen) rhpvorderman@tuxminator:~/PycharmProjects/xopen$ cat ~/test/5millionreads_R1.fastq | python -c 'import xopen; f=xopen.xopen("/dev/stdin", "rt"); print(f.read())' | wc -l
20000001
(xopen) rhpvorderman@tuxminator:~/PycharmProjects/xopen$
Xopen 1.9.0 performs as it should (the extra newline is added by print)
xopen2.0.0 misses some data? Which is really weird as all the xopen tests pass. I will see if I can fix this issue.
I will yank the 2.0.0 release. This is quite serious. Ping @marcelm
Ah - I hadn't taken the next step of seeing if this was an xopen bug vs cutadapt needing a tweak for an xopen change.
Let's close this and focus on https://github.com/pycompression/xopen/issues/157
I've excluded v2.0.0 on my development branch so my CI works, but that is only a stopgap:
https://github.com/peterjc/thapbi-pict/commit/5b7466da9d3cb056177c627150b8a3ab4f42f109
Yanking the xopen 2.0.0 release seems prudent, thanks - this is more serious that just a cutadapt issue as I first assumed 👍
Working with xopen 1.9.0 (and older), running here on macOS:
Using sample file tests/ncbi-import/multiple_hmm.fasta with this command which outputs 5 of FASTA entries via stdin:
Broken when update to xopen 2.0.0 (released 2024-03-26 https://pypi.org/project/xopen/#history - yesterday):
Also using
/dev/stdin
is broken:This might be related to #772, but the timing doesn't fit with xopen 2.0.0 being released yesterday.