CALQ

Coverage-Adaptive Lossy Quality value compression

This is the official repository for the development of the CALQ software. It is hosted at GitHub (https://github.com/voges/calq).

Build instructions

We provide a CMakeLists.txt to build the CALQ with CMake (https://cmake.org/). At least CMake version 3.1 is required.

CALQ has been tested on the following systems:

openSUSE Leap 42.1 with GCC 4.8.5
openSUSE Tumbleweed 20170308 with GCC 6.3.1
macOS Sierra (version 10.12.3) with Apple LLVM (i.e., Clang) version 8.0.0.

Clone the CALQ repository with

git clone https://github.com/voges/calq.git

Build the executable from the command line with the following commands; alternatively use the CMake GUI.

cd calq
mkdir build
cd build
cmake ..
make

This generates a CALQ executable named calq in the build folder.

Usage examples

As usual, a list of the available command line options can be obtained via calq --help or calq -h.

Compression

The CALQ encoder accepts input files in the SAM format (see also https://github.com/samtools/hts-specs).

Basically, the following command can be used to compress the quality values from the SAM file file.sam.

calq file.sam

By default, the compressed quality values are written to the file file.sam.cq. Furthermore, the CALQ encoder uses the following parameters by default:

-b 10000 | --blockSize 10000 (block size in number of SAM records, i.e., alignments),
-p 2 | --polyploidy 2 (sequence reads from a diploid organism are assumed),
-q Illumina-1.8+ | --qualityValueType Illumina-1.8+ (quality values in the Illumina 1.8+ format (Phred+33, i.e., [0, 41] + 33) are assumed).

Thus, the above command is equivalent to the following command.

calq -q Illumina 1.8+ -p 2 -b 10000 file.sam -o file.sam.cq

Decompression

To perform the decompression of the file file.sam.cq, the CALQ decoder requires the alignment information, namely the mapping positions (POS), the CIGAR strings, and the reference sequence name(s) (RNAME). This information can be passed to the CALQ decoder with the argument -s file.sam. The switch -d invokes the decoder.

calq -d -s file.sam file.sam.cq

By default, the reconstructed quality values are written to the file file.sam.cq.qual.

Thus, the above command is equivalent to the following command.

calq -d -s file.sam file.sam.cq -o file.sam.cq.qual

Finally, a SAM file containing the reconstructed quality values can be produced with the Python script replace_qual_sam.py. This and other supplementary scripts can be found in the folder src/ngstools.

replace_qual_sam.py file.sam file.sam.cq.qual 1> file.sam.cq.sam

This produces a new SAM file file.sam.cq.sam containing the reconstructed quality values.

Who do I talk to?

Jan Voges <voges@tnt.uni-hannover.de>

Mikel Hernaez <mhernaez@illinois.edu>

hut / calq