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The code is only lightly tested, but hopefully feature complete. Before merging, the configury (currently GNU Make-specific) will need to be improved. This awaits a configure script and probably --enable-irods and/or --with-irods=IRODS_HOME configure options.
Conflicts: Makefile hfile.c
autoconf. The intention is that aside from running autoconf, all
previous Makefile behaviour is preserved.
The original Makefile becomes Makefile.in, preserving the custom
build behaviour. The package version and SO version are configured
in configure.ac.
iRODS is off by default and enabled using --with-irods=/path/to/irods
or just --with-irods where a default path is used.
A -O option has been added to test_view and
"test_view.pl irods" will run test_view.pl as normal, but writing
its results directly into iRODS.
The Travis config is updated to run configure.
autoconf to generate an optional config_auto.mk file to include.
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I've modified this pull request to restore the original Makefile, but with an optional included makefile |
This merge commit adds --with-irods[=DIR] support in configure.ac and config.mk.in. Addresses PR #146 with the exception of test harness iRODS support.
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Thanks for pushing this, Keith! I've now merged the iRODS backend. The eventual configury, ermm..., doesn't bear a lot of resemblance to the configury in your pull request, but yours was very useful as a proof-of-concept and to crib parts from. I haven't merged the test harness stuff, as that seems somewhat separate (and perhaps bound up with our local environment?). Please resurrect it as a new pull request if you wish, and we can merge it (more quickly this time!) post-1.2. |
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Thanks for merging. Regarding the tests - they are independent of our local environment. Of course, they could be destructive if run somewhere else without care (the post-test cleanup target will irm files matching a pattern in the iRODS cwd). All they do is allow the existing suite of test_view tests to be run while writing the data into iRODS. It's somewhat ugly, but I wanted some tests for the pull request while still focussing mainly on the autoconf part. |
ghost
deleted the
Changelog from htscodecs: - Prevent use of unaligned 16-bit integers from memmove. (PR samtools#145 Robert Davies) - Add missing support for X_CAT in arithmetic codec. (PR samtools#146; Issue samtools#144 Michael Macias)
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An initial pass at adding configuration support for iRODS using autoconf. The intention
is that aside from running autoconf, all previous Makefile behaviour is preserved.
build behaviour. The package version and SO version are configured
in configure.ac.
or just --with-irods where a default path is used.
"test_view.pl irods" will run test_view.pl as normal, but writing
its results directly into iRODS.