v0.1.3

Dev (#37)

* update

* check for no reads passing filters

* Fix odd too many files open error in bigtools by not reading from stdin

* bump version

* consistent param order

* explicit threads

* run decorate early

* bump bigtools

* only use major and minor version

* consistent param order

* explicit threads

* run decorate early

* bump bigtools

* only use major and minor version

* fmt

* more mem

---------

Co-authored-by: Mitchell R. Vollger <mvollger@gmai.com>

v0.1.2 (#36)

* update

* check for no reads passing filters

* Fix odd too many files open error in bigtools by not reading from stdin

* bump version

---------

Co-authored-by: Mitchell R. Vollger <mvollger@gmai.com>

v0.1.1

Added more informative error messages if an FDR distribution cannot be made or there is not enough coverage.

v0.1.0: Working to the next release (#30)

This is a major refactor of the FIRE pipeline and the naming of its outputs and will represent the v0.1.0 of the software.

There are no changes to the underlying methods or ideas, but I have made significant efforts to speed up the software and reduce dependencies while increasing reliability.

v0.0.7

This release of FIRE will be more robust for denovo assemblies.

Some feats:

• Save the Fiber-seq data in cram format
• Replace ucsc utilities with bigtools
• Replace some bedtools opts with gia
• Switch to polars for coverage calculation
• Rename config options to uppercase variables
• fix #28 incorrect counts in a plot
• fix #26 so that fire appears to be deterministic now; however, this is not yet guaranteed.

Release for code using in the multi-ome manuscript

multi-ome-v0.1

update

Improve support of custom assemblies

• add optional filtering by contig length
• make merge commands more robust to 1000s of contigs
• add a missing sort in the coverage bedgraph
• reduce memory needed for the median calculation

Minor patch that fixes a corner case in median coverage calculation

Fixes a minor cornor case in the median coverage calculation, this does not affect the FDR calculations, just the median coverage calculation.

v0.0.4 Fix missing fibers in the FDR calculation

Due to a bad join, fibers without FIRE elements were missing from FDR and coverage calculations. This PR fixes that. All analyses that used the FDR pipeline (October 19th, 2023) should be repeated with this fix. Apologies to all.

v0.0.3 switching the the ft fire model

tagging pre ft fire