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!
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
- Per the
- As specified in the CRAM's
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)
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$(echo ~/local/lib/pkgconfig))
If the source tree was cloned from the git repository, run:
./autogen.sh(not required if you unpacked from a tar distribution)
Make and change to a
mkdir build && cd build
--prefixappropriately; in this case,
../configure HTSLIB_LDFLAGS="$(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)
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
"cramp", an excruciating pain caused by involuntary contraction, which
happens to contain the word "CRAM".
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/.