CHISEL NONORMAL and GC with multi-lane-fixed prep

Fix the same ordering for multiple lanes of sequencing in chisel_prep

CHISEL NONORMAL and GC with new chisel_rdr command

Adding chisel_rdr command to only compute RDRs across all cells.

CHISEL NONORMAL and GC fixes for HPCs

This sub-release include fixes for proper running on HPCs:

• fix the number of threads in submodules to 1
• use Agg plotting engine for matplotlib

Full Changelog: v1.1.1...v1.1.2

CHISEL nonormal with pseudonormal fix

Fix errors related to pseudonormal command in the new CHISEL nonormal version.

Full Changelog: v1.1...v1.1.1

Nonormal CHISEL command and additional GC correction

The main novel features of this version v1.1 are:

• A new nonormal CHISEL command, which allows running CHISEL without a mathed-normal sample
• The possibility to add additional GC correction
• A statistical test to correct clear switch errors in the given phasing
• Improved method for clone identification
• Additional improvements in calling of copy numbers (e.g., proper dealing with homozygous deletions)

Complete version with RDRs and BAFs plots

The following complete version includes two additional fixes to all the last enhancements:

1. Add the barcodeonly option to the command chisel_prep for only generating barcodes without running the aligning pipeline;
2. Add plots of the raw RDRs and BAFs.

New prep and bedding commands

This release introduces two new commands to CHISEL: chisel_prep for the automatic generation of input barcoded BAM files, and chisel_bedding for generating BED files from CHISEL results. Moreover, the release introduces several minor fixes, including:

• restructuring of source code for proper packaging
• fix to random seeding for deterministic results
• improve efficiency of bcftools by streaming genomic positions
• fixes to some of the plotting functions (colormaps had error in some special cases)

Fix setup version and file paths

v0.0.4

Fix package version in setup

Fix setup errors

v0.0.3

Fix wrong versions in setuptools

Correct script names

Correct script names for the CHISEL commands for correct installation