Initial commit for project besst2
Adding some initial modules for treating sequence objects and storing a scaffold graph.
added interval class for finding most reliable neighbors in the scaffold graph. Modified test.py
Continued implementation.
Finished small milestone: from a set of premade sequences, obtain a scaffold. More error testing needs to be done.
Started implementing main script and input module for generating input to main.
Changed to more clear structure in interval module
Started working on test data for besst2
Fixed bug in graph pruning edges. Added tests.
Overlap_parameter added. More test files added. Gap estimations are given in input file
added breakpoint checking for contigs. the most naive one
Added printing of subseqs/contigs to "sequence file.
Next steps are adding link file and clean up preprocess module.
Cleanup by following the points in evernote"
besst2 can now create a link.txt file from a bam file.
besst2 can now run a complete scaffolding run from just a bam file and
a contig file. Now its time to document, bugfix and fix all TODOs.
besst2 now naively takes care of cycles. This should be looked over again.
It also handles basic gap estimates from observations. Still need to document
fix todo's and eventually ship some of the functionality into the classes.
Now, the two main script look a bit messy.
some small changes. See previous commit for development status.