Software releases and source code
The full source code for the software can be found on gitHub at https://github.com/NigelDyer/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 |
| 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 |
| 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 |