Software releases and source code

The source code for the core software can be found on gitHub at https://github.com/WarwickBioinformaticsRTP/LiBiNorm

In order to build the software on Linux or a MAC it is necessary to clone the following additional repositories alongside the LiBiNorm directory:

For windows, as well as these two repositories it is also necessary to clone this additional repository:

https://github.com/WarwickBioinformaticsRTP/zlib

The Makefile in the LiBiNorm supports 'make release', 'make debug' and 'make clean'

The Microsoft Visual Studio LiBiNorm.sln file in the LiBiNorm directory supports building x64 release and debug versions of LiBiNorm

Version history:

Version

Date

Description

1.8.1

16/3/17

Initial beta release

1.9.0

22/3/17

Add -o option for outputting bam files with reads marked with associated feature

1.10.0

7/7/17

Slight change to calculation of _bias.txt output - includes changes to LiBiNormPlot.R R code

1.11.0

29/7/17

Improved consistency with htseq-count when the bam file is position ordered. Introduce -n none mode, which produces the same output as -z but without the htseq-compatibility tweaks

1.11.1

2/8/17

-w and -x debug options exchanged. -i debug option changed to -v to avoid clash of command identifiers

1.11.2

11/8/17

Improved recognition and parsing of gff, gff3 and gtf files. Options specific to NCBI originated files are only enabled if the header identifies the data as NCBI originated.

1.11.3

13/10/17

Add debug build option that allows a landscape file to be generated that only contains the reads used for parameter discovery

1.11.4

6/11/17

Seed can be set in model as well as count mode
Allow feature type (-t) to be gene.

2.0

3/5/18

Some changes to command line parameters in line with paper reissue. Change to <filename>_bias.txt output format. Add LiBiNorm bed and LiBiNorm fasta modes

2.1

10/2/20

Correct help text. Default mode is different when -z option is used

2.2

11/3/20

In -z htseq-compatible mode all sources ("havana" etc) are used
Linux -c option now works

2.3

12/3/20

-u <fileroot> -j in -z mode now outputs an expression file that includes TPM etc values

2.4

26/3/20

__alignment_not_unique counts now consistent with htseq-count 0.11.
Temporary files now in local directory if -c option used
Temporary directory now deleted at the end of a run.
Bug fix: A source of a small occasional discrepancy between position ordered and name ordered results now fixed.

2.5

6/12/20

Change the way that chromosomes are identified internally to allow LiBiNorm to handle a variety of different ways of identifying chromosomes in gtf/gff and bam files
Allow gff/gtf files that do not have chromosome identity lines to be used