13 Amp

Keep your lab, office or datacentre warm with this userspace CRAM-to-BAM translation virtual filesystem, which trades the cost of disk space for CPU, memory and time...so much time!

Usage

13amp MOUNTPOINT [OPTIONS]

Viable options are:

-S, --source=DIR|URL   Source directory (defaults to CWD)
-h, --help             This helpful text
    --version          Print version

The source directory may also be provided as a mount option (e.g., in your fstab). When pointing to a URL, this is expected to resolve to a manifest file (i.e., a file of CRAM URLs).

Note that the search order for CRAM reference files is:

• Per the REF_CACHE environment variable;
• Per the REF_PATH environment variable;
• As specified in the CRAM's UR header tag.

If none of the above are found, then ~/.cache will be used. This directory will also be used for the CRAM stat cache, unless the --cache option or CRAMP_CACHE environment variable is set.

Quick Build (with pkg-config)

1. Set your PKG_CONFIG_PATH appropriately (e.g. export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$(echo ~/local/lib/pkgconfig))

2. If the source tree was cloned from the git repository, run: ./autogen.sh (not required if you unpacked from a tar distribution)

3. Make and change to a build subdirectory: mkdir build && cd build

4. Run configure (setting --prefix appropriately; in this case, installing into ~/local):

   ../configure HTSLIB_LDFLAGS="$(pkg-config --libs htslib)" \
                 HTSLIB_CFLAGS="$(pkg-config --cflags htslib)" \
                 FUSE_LDFLAGS="$(pkg-config --libs fuse)" \
                 FUSE_CFLAGS="$(pkg-config --cflags fuse)" \
                 --prefix=$(echo ~/local)

5. make install

Etymology

13 Amp uses FUSE (Filesystem in USErspace) to provide the filesystem layer; therein lies the obvious connection. Moreover, 13 is the ASCII and Unicode character code for a carriage return, or CR. Hence "cramp", an excruciating pain caused by involuntary contraction, which happens to contain the word "CRAM".

License

Copyright (c) 2015 Genome Research Limited

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.