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Software releases and source code

The full source code for the software can be found on gitHub at

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 assocociated 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 debgug 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