Add additional checks for non-seekable input - #707
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Pre-preocessing checks for adapters etc. by reading some of the input then rewinding the file, and this is turned off for /dev/stdin explicitly because rewinds won't work. Unfortunately, this doesn't catch process substitution inputs (e.g. `<(zcat file.fq.gz)`) which then silently drop data when the rewinds fail. This commit introduces a new helper function which checks whether the file descriptor is rewindable, turning off evaluation if not.
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This will fix this longstanding issue: #183 |
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Pre-preocessing evaluation searches for adapters etc. by reading some of the input then rewinding the file, and this is turned off for /dev/stdin explicitly because rewinds won't work. Unfortunately, this doesn't catch process substitution inputs (e.g.
<(zcat file.fq.gz)) which then silently drop data when the rewinds fail.This commit introduces a new helper function which checks whether the file descriptor is rewindable, turning off evaluation if not.