Version 1.2.5.
Major change in the way the sequences are Mapped. Now a simple needleman wunsch inspired global alignment function is used to check if a second up to 32bp long sequence would be a match (in case it is not a perfect match). This gives a significantly higher fraction of reads that map to a know gene in the targeted version. It has nether been checked extensively not applied to multiple datasets, but it is looking good.
This is the final version of the 1.2.5 branch.
The final version contains the first draft of the TE analysis pipeline consisting of create_index_te and te_analysis.
10x single cell data can now also be analyzed using the Rustody programs quantify_rustody_multi and te_analysis.
Please mention - for te_analysis 10x is the default mode.
During the development of this version the index/mapper has reached a mature state. The (expression) data is now comparable with STAR output. Rustody is not built to produce bam files.