Delete the "samtools import" subcommand. #1185
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jkbonfield
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This was deleted from the help / usage statements in 2009 (cc207d8) between 0.1.5 and 0.1.6. Thus it has never been a documented command since the official launch of Samtools. Import was just a wrapper around view, but the wrapper broke when we added PG headers. While a fix is trivial, this PR simply removes the dead and untested code instead. Fixes samtools#1183 in as far as turning the segmentation fault into a handled usage error instead.
daviesrob
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Could we be nice and show the new syntax to the user? becomes |
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I'd suggest not being nice here, since any user doing this is likely doing so many other things in antiquated ways that they should rethink everything. |
The legacy import command was broken in Samtools 1.10 (hat tip @mr-c) and has been removed from future Samtools (see samtools/samtools#1185). Use the equivalent `samtools view` command instead. Update 00README.txt to the current text in samtools/examples/00README.txt that it was copied from, and delete the samtools command samples as they are not relevant for pysam.
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Exactly my thought @dpryan79. I wanted the user to think about what they're doing and look at the man page to see all the other features of view and to decide whether their usage is appropriate rather than suggest more cargo-cult cut paste non-thinking work. Let's face it, since import was supported there have been new file formats, new SAM flags (SUPPLEMENTARY, etc) and so on. Also IMO this is all a storm in a teacup. The fact is there have been over 10,000 installs of samtools with the broken import command and not a single user reported it being broken. We got acknowledgement an automatic test harness breaking, but it would appear in day to day usage this command has dropped out of common usage. |
The legacy import command was broken in Samtools 1.10 (hat tip @mr-c) and has been removed from future Samtools (see samtools/samtools#1185). Use the equivalent `samtools view` command instead. Update 00README.txt to the current text in samtools/examples/00README.txt that it was copied from, and delete the samtools command samples as they are not relevant for pysam.
Remove samimport / `samtools import`, which has been removed from upstream samtools (samtools/samtools#1185).
This was deleted from the help / usage statements in 2009 (cc207d8)
between 0.1.5 and 0.1.6. Thus it has never been a documented command
since the official launch of Samtools.
Import was just a wrapper around view, but the wrapper broke when we
added PG headers. While a fix is trivial, this PR simply removes the
dead and untested code instead.
Fixes #1183 in as far as turning the segmentation fault into a handled
usage error instead.