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Staden Package "io_lib" (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.
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MSVC_includes Moved the MSC_includes/windows/* files up one level. Mar 24, 2016
docs Moved io_lib from staden source tree into it's own top-level Jul 28, 2009
htscodecs @ 83b1db0 Bump htscodecs revision Jul 17, 2019
io_lib Fix a gcc optimiser buglet. Aug 2, 2019
m4 Moved the "external" CRAM codecs into their own sub-package. Jul 3, 2019
man Rejig the compression profiles. May 8, 2019
progs Silenced a bunch of gcc 9.1.0 warnings. Aug 2, 2019
tests Moved the "external" CRAM codecs into their own sub-package. Jul 3, 2019
.gitignore Minor updates related to switching to git. Dec 14, 2016
.gitmodules Fix following htscodecs update (removal of fqz_rec.qual field). Jul 3, 2019
.travis.yml Fixed travis use of git submodule. Jul 3, 2019
CHANGES Misc doc updates May 13, 2019
COPYRIGHT Added GRL copyright too due to appropriate local requirements. Oct 18, 2013
Makefile.am Renames hts_codecs to htscodecs for consistency with htslib, htsget, etc Jul 3, 2019
README.md Added CRAM 2.0 to the simple benchmarks. May 16, 2019
acinclude.m4 Fixed LDFLAGS typo. May 29, 2019
bootstrap Fixed travis use of git submodule. Jul 3, 2019
configure.ac Renames hts_codecs to htscodecs for consistency with htslib, htsget, etc Jul 3, 2019
io_lib-config.in Fixed -lread to be -lstaden-read Jul 31, 2009
io_lib.m4 Moved io_lib from staden source tree into it's own top-level Jul 28, 2009
options.mk Purged CTF from the source tree. Oct 18, 2013

README.md

Io_lib: Version 1.14.11

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.

This branch (as of 13th May 2019)

  • CRAM: Added compression profiles to scramble. Specify with -X profile where "profile" is one of fast, normal (default), small or archive.

  • Improved CRAM v3.1/4.0 codec compression ratios and speed. See below for a small benchmark.

  • CRAM (EXPERIMENTAL): scramble -E permits use of a consensus as the embedded reference instead of real reference. Note this breaks some CRAM decoders, so will probably be reserved for CRAM v4.0.

Version 1.14.11 (16th October 2018)

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.

Technology Demo: CRAM 3.1 and 4.0

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. It is likely CRAM v4.0 will be official significantly later, but we plan on v3.1 being a recognised GA4GH standard this year.

By default enabling either of these will also enable the new codecs. Which codecs are used also depends on the profile specified (eg via "-X small"). Some of the new codecs are considerably slower, especially at decompression, but by default CRAM 3.1 aims to be comparable speed to 3.0. Note the profiles also change the granularity of random access (1k, 10k, 25k, 100k for fast, normal, small and archive respectively).

Here are some example file sizes and timings with different codecs and levels on 10 million 150bp NovaSeq reads, single threaded. Decode timing is checked using "scram_flagstat -b". Tests were performed on an Intel i5-4570 processor at 3.2GHz.

Scramble opts. Size(MB) Enc(s) Dec(s) Codecs used
-O bam 531.9 92.3 7.5 bgzf(zlib)
-O bam 539.5 48.5 3.7 bgzf(libdeflate)
-V2.0 257.0 43.5 10.9 (default)
-V2.0 -X fast 302.6 37.0 12.1 (default, level 1)
-V2.0 -X small 216.3 126.9 31.2 bzip2
-V3.0 223.7 39.9 9.8 (default)
-V3.0 -X fast 274.0 35.6 10.6 (default, level 1)
-V3.0 -X small 212.2 94.3 18.0 bzip2
-V3.0 -X archive 209.3 106.6 17.6 bzip2, lzma
-V3.1 186.5 38.3 8.9 rANS++,tok3
-V3.1 -X fast 282.7 29.5 9.2 rANS++
-V3.1 -X small 177.0 78.7 33.3 rANS++,tok3,fqz
-V3.1 -X archive 172.1 137.2 34.9 rANS++,tok3,fqz,bzip2,arith

Building

Prerequisites

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

Zlib

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).

Libdeflate

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

Git clone

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.

Linux

We use the GNU autoconf build mechanism.

To build:

  1. ./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

  1. make (or gmake)

This will build the sources.

CFLAGS may also be changed a build time using (eg): make 'CFLAGS=-g ...'

  1. make install

The default installation location is /usr/local/bin and /usr/local/lib. These can be changed with the --prefix option to "configure".

Windows

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.

Libbsc

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. **

MacOS X

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
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