This README file will detail the usage and purpose of the SAM compressor AliCo.

AliCo is a compressor and decompressor for SAM files and reference files.

To make the program, download the code from GitHub. Make sure to have a version of cmake 3.5.0 or more recent installed and loaded. Make sure to be in the directory Streamer_SAMfiles. The best practice for cmake is to create an empty directory "build-dir", change to that directory, and run "cmake .." to create the Makefile in "Streamer_SAMfiles". When that is done, change to the parent directory and simply run "make" to create the executable program SAMStreamer.

Running "./SAMStreamer -h" will bring up this help message:

Usage: ./SAMStreamer (options) [input file] [output] [ref file] Options are: -x : Regenerate file from compressed file -c [ratio] : Compress using [ratio] bits per bit of input entropy per symbol -d [rate] : Decompress and Download file from remote [output] -u [rate] : Compress and Upload file to remote [output] -s [rate] : Stream file to remote [output] -D [M|L|A] : Optimize for MSE, Log(1+L1), L1 distortions, respectively (default: MSE) -q : CALQ Mode -p [num] : Set the polyploidy value for CALQ (default: 2) -a [num] : Set the max quality value for CALQ (default: 41) -i [num] : Set the min quality value for CALQ (default: 0) -o [num] : Set the quality value offset for CALQ (default: 33) -e : Compress reference file along with SAM file -m : Decompress reference file along with SAM file -h : Print this help

The default is compression mode (-c), so this need not be specified for lossless compression.

For normal compression mode, run "./SAMStreamer ". This will create a few files in the output directory. "headers" contains the compressed headers and "mapped_reads" contains the compressed mapped reads from the SAM file. "unmapped_reads.gz" is a file uncompressed by the SAMStreamer but compressed by gzip.

For normal decompression mode, run "./SAMStreamer ". This reads the directory automatically for the correct files and writes the final decompressed file to the specified location.

OPTIONS -c [ratio], compression Specify the bits per bit of input entropy per symbol in compression mode.

-u, upload
    Compress and upload the file to remote.

-s, stream
    Stream the file to remote.

-D [type], distortion optimization
    Specify the distortion optimization.  The types are:
        M : MSE distortions
        L : Log(1+L1) distortions
        A : L1 distortions
        If not specified, the default is MSE.

-x, decompress
    Decompress a compressed SAM file.

-e, compress reference file
    Compress the reference file as well as the SAM file. This creates the additional files "reference_num" and "reference_comp" which contain compressed information about the reference file.

-m, decompress reference file
    Decompress the reference file which has been compressed by the above method. There is no reference file argument required in this mode, simply run "./SAMStreamer -m <input directory> <regenerated SAM file name>". This will create the regenerated reference file under the name "reference_local.fa" in the input directory specified.

CALQ OPTIONS

-q, CALQ compression
    Compress the quality values with CALQ. This creates an additional file in the output directory "quality_values_calq" which contains the compressed quality values.

-z, CALQ Decompression
    Decompress the quality values with CALQ. Usage: "./SAMStreamer -z <input Directory> <output file name> <reference file name>".

-p, polyploidy
    Set the polyploidy value for CALQ (2 by default).

-a, max quality value
    Set the maximum quality value for CALQ (41 by default).

-i, min quality value
    Set the minimum quality value for CALQ (0 by default).

-o, quality value offset
    Set the quality value offset for CALQ (33 by default).