Io_lib is a library of file reading and writing code to provide a general purpose SAM/BAM/CRAM, trace file (and Experiment File) reading interface. Programmatically {S,B,CR}AM can be manipulated using the scram_*() API functions while DNA Chromatogram ("trace") files can be read using the read_reading() function.
It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.
The directories below here contain the io_lib code. These support the following file formats:
SAM/BAM sequence files
CRAM sequence files
SCF trace files
ABI trace files
ALF trace files
ZTR trace files
SFF trace archives
SRF trace archives
Experiment files
Plain text files
These link together to form a single "libstaden-read" library supporting all the file formats via a single read_reading (or fread_reading or mfread_reading) function call and analogous write_reading functions too. See the file include/Read.h for the generic 'Read' structure.
See the CHANGES for a summary of older updates or git logs for the full details.
Updates:
- CRAM: http(s) queries now honour redirects. The User-Agent header is also set, which is necessary in some proxies.
Bug fixes:
-
CRAM: fix to major range query bug introduced in 1.14.10.
-
CRAM: more bug fixing on range queries when multi-threading (EOF detection).
-
The test harness now works correctly in bourne shell, without using bashisms.
Updates:
-
BAM: Libdeflate support (https://github.com/ebiggers/libdeflate). This library is significantly faster than zlib, so it is a good alternative to the Cloudflare and/or Intel libraries.
See below for details.
-
CRAM EXPERIMENTAL: Added custom quality and identifier codecs. Also added the ability to use libbsc as a general purpose codec.
These are NOT OFFICIAL and so not enabled by default (version 3.0). However as a technology demonstration only, they are available with scramble -V3.1 or -V4.0 for evaluation and to promote discussion on future CRAM formats. Do not use these on production data.
Implementations of the codecs and CRAM version 4.0 layout are liable to change without prior warning.
-
CRAM: name sorted files now automatically switch to non-ref mode.
Bug fixes:
-
CRAM: Considerable fixes to multi-threading.
- Using more than 1 slice per container with threading now works.
- Removal of race conditions when using CRAM_OPT_REQUIRED_FIELDS.
- Combinations of ref and no-ref mode in adjacent containers.
- Other misc. threading bugs.
-
Corrected end-of-range check in some scenarios.
-
CRAM: bug fix to index creation when a slice contains exactly one alignment.
-
SAM: fixed parsing of illegal sequence characters (eg "Z"). These are now treated as "N" and not "=".
-
BAM/SAM: protect against out of bound CIGAR operations.
-
CRAM: hardening of rANS codec against malicious input. Also fixed a very rare frequency renormalisation case.
-
CRAM: fix with range queries used in conjuction with turning off sequence retrieval (via CRAM_OPT_REQUIRED_FIELDS).
-
Improved test harness for Windows and some header file problems.
-
Fixed bgzip on big endian systems. (Debian bugs 876839, 876840)
The current official GA4GH CRAM version is 3.0.
For purposes of EVALUATION ONLY this release of io_lib includes CRAM version 3.1, with new compression codecs (but is otherwise identical file layout to 3.0), and 4.0 with a few additional format modifications, such as 64-bit sizes.
They can be turned on using e.g. scramble -V3.1 or scramble -V4.0.
By default enabling either of these will also enable the new codecs, bar libbsc (see below for how to compile with this). These new codecs are slower, but will not be used at lighter levels of compression. So for example "scramble -V4.0 -4 in.bam out.cram" will only use the same codecs available in CRAM 3.0 bar the fast new rANS variants (rANS++).
Here are some example file sizes and timings with different codecs and levels on 10 million NovaSeq reads, with 4 threads (-t4). Decode timing is checked using "scram_flagstat -b -t4". Tests were performed on an Intel i5-4570 processor at 3.2GHz.
| Scramble opts. | Size | Enc(s) | Dec(s) | Codecs used |
|---|---|---|---|---|
| -V3.0 | 224743050 | 12.9 | 3.8 | (default) |
| -V3.0 -7jZ | 211734953 | 105.9 | 5.4 | bzip2, lzma |
| -V3.1 -4 | 226888980 | 13.2 | 3.8 | rANS++ |
| -V3.1 | 187238214 | 35.8 | 12.8 | tok3,fqz,rANS++ |
| -V3.1 -7J | 180217109 | 49.2 | 25.6 | tok3,fqz,rANS++,libbsc |
| -V4.0 -4 | 211515487 | 15.6 | 3.8 | rANS++ |
| -V4.0 | 182657527 | 34.9 | 13.5 | tok3,fqz,rANS++ |
| -V4.0 -7J | 178819704 | 46.5 | 19.6 | tok3,fqz,rANS++,libbsc |
You will need a C compiler, a Unix "make" program plus zlib, bzip2 and lzma libraries and associated development packages (including C header files). The appropriate operating system package names and comands differ per system. On Debian Linux derived systems use the command below (or build and install your own copies from source):
sudo apt-get install make zlib1g-dev libbz2-dev liblzma-dev
On RedHat derived systems the package names differ:
sudo yum install make zlib-devel bzip2-devel xz-devel
This code makes heavy use of the Deflate algorithm, assuming a Zlib interface. The native Zlib bundled with most systems is now rather old and better optimised versions exist for certain platforms (e.g. using the SSE instructions on Intel and AMD CPUs).
Therefore the --with-zlib=/path/to/zlib configure option may be used to point to a different Zlib. I have tested it with the vanilla zlib, Intel's zlib and CloudFlare's Zlib. Of the three it appears the CloudFlare one has the quickest implementation, but mileage may vary depending on OS and CPU.
CloudFlare: https://github.com/cloudflare/zlib Intel: https://github.com/jtkukunas/zlib Zlib-ng: https://github.com/Dead2/zlib-ng
The Zlib-ng one needs configuring with --zlib-compat and when you build Io_lib you will need to define -DWITH_GZFILEOP too. It also doesn't work well when used in conjunction with LD_PRELOAD. Therefore I wouldn't recommend it for now.
If you are using the CloudFlare implementation, you may also want to disable the CRC implementation in this code if your CloudFlare zlib was built with PCLMUL support as their implementation is faster. Otherwise the CRC here is quicker than Zlib's own version. Building io_lib with the internal CRC code disabled is done with ./configure --disable-own-crc (or CFLAGS=-UIOLIB_CRC).
The BAM reading and writing also has optional support for the libdeflate library (https://github.com/ebiggers/libdeflate). This can be used instead of an optimised zlib (see above), and generally is slightly faster. Build using:
./configure --with-libdeflate=/path
We recommend building from a release tarball, which has the configure script already created for you. However if you wish to build from the latest code and have done a "git clone" then you will need to create the configure script yourself using autotools:
autoreconf -i
This program may not be on your system. If it fails, then install autoconf, automake and libtool packages; see above for example OS-specific installation commands.
We use the GNU autoconf build mechanism.
To build:
- ./configure
"./configure --help" will give a list of the options for GNU autoconf. For modifying the compiler options or flags you may wish to redefine the CC or CFLAGS variable.
Eg (in sh or bash): CC=cc CFLAGS=-g ./configure
- make (or gmake)
This will build the sources.
CFLAGS may also be changed a build time using (eg): make 'CFLAGS=-g ...'
- make install
The default installation location is /usr/local/bin and /usr/local/lib. These can be changed with the --prefix option to "configure".
Under Microsoft Windows we recommend the use of MSYS and MINGW as a build environment.
These contain enough tools to build using the configure script as per Linux. The latest msys can be downloaded here:
http://repo.msys2.org/distrib/msys2-x86_64-latest.exe
Once installed and setup ("pacman -Syu"; close window & relaunch msys; "pacman -Syu" again), install mingw64 compilers via "pacman -S --needed man base-devel git mingw-w64-x86_64-toolchain".
This should then be sufficient to configure and compile. However note that you may need to use "./configure --disable-shared" for the test harness to work due to deficiences in the libtool wrapper script.
If you wish to use Microsoft Visual Studio you may need to add the MSVC_includes subdirectory to your C include search path. This adds several missing header files (eg unistd.h and sys/time.h) needed to build this software. We do not have a MSVC project file available and have not tested the build under this environment for a number of years.
In this case you will also need to copy io_lib/os.h.in to io_lib/os.h and either remove the @SET_ENDIAN@ and adjacent @ lines (as these are normally filled out for you by autoconf) or add -DNO_AUTOCONF to your compiler options.
The code should also build cleanly under a cross-compiler. This has not been tested recently, but a past successful invocation was:
./configure \
--host=x86_64-w64-mingw32 \
--prefix=$DIST \
--with-io_lib=$DIST \
--with-tcl=$DIST/lib \
--with-tk=$DIST/lib \
--with-tklib=$DIST/lib/tklib0.5 \
--with-zlib=$DIST \
LDFLAGS=-L$DIST/lib
with $DIST being pre-populated with already built and installed 3rd party dependencies, some from MSYS mentioned above.
This is experimental, just to see what we can get with a high quality compression engine in CRAM. It's hard to build right now, especially given it's a C++ library and our code is C. The hacky solution now is (linux) e.g.:
../configure
CPPFLAGS=-I$HOME/ftp/compression/libbsc
LDFLAGS="-L$HOME/ftp/compression/libbsc -fopenmp"
LIBS=-lstdc++
Enable it using scramble -J, but note this requires experimental CRAM versions 3.1 or 4.0.
** Neither of these should be used for production data. **
The configure script should work by default, but if you are attempting to build FAT binaries to work on both i386 and ppc targets you'll need to disable dependency tracking. Ie:
CFLAGS="-arch i386 -arch ppc" LDFLAGS="-arch i386 -arch ppc" \
../configure --disable-dependency-tracking