Version 1.3.2

Set parameter "starting_it" to -1 by default, as otherwise the first chunk of the bed file would be skipped.

Version 1.3.1

Added a parameter -d to apply_model_multiprocess.py. This script has a tendency to hang unexpectedly (especially when using many CPU cores). Using this parameter, you can specify an existing temporary directory with the footprint-bed file chunks from a previous, failed run (in your original outdir). The script will then read and skip quickly past chunks of the m6a bed already footprint called, and then resume where it had left off.

FiberHMM v1.3

Added a new parameter, -e to train and apply model scripts. This allows the user to set a minimum level of methylation required for a read to be used in training or to be kept after the model application. This is helpful if there are a subset of reads with very low methylation due to experimental issues.

Adjusted apply and train model scripts to use the reference-based position of m6a instead of the read-based position. This resolves issues related to poorly aligned reads having methylations and footprints outside of the expected range.

FiberHMM v1.2.1

Readded the first/last methylation trim to fix an error.

FiberHMM v1.2

Major changes:

1. Added a new parameter to train_model and apply_model, -e. This allows reads to be masked by n bp at either end with 0% methylation probability. This is necessary due to the inability of fibertools to call methylations in the first and last 8 bp of the read.
2. Added a folder with example input, intermediate, and output files to allow for testing of the scripts.
3. Added a folder to store pretrained models.

Small changes:

1. Fixed a bug where column names of BlockSizes/BlockStarts were swapped in the final output
2. Standardized the -b flag across all scripts
3. Removed a reference in the Readme to multiple input files for apply_model
4. Added parameter -e, as noted above.
5. Changed apply_model.py to output a single bed file instead of individual bed files for each chromosome (matching apply_model_multiprocess.py)

FiberHMM v1.1

Made major changes to apply_model:

• Now reads the input bed in chunks and writes processed reads as tempfiles to minimize memory usage.
• Simplified the processing of the reads into the bed12 format, significantly speeding up the script.

Added a parallelized version of apply_model:

• Linearly increases speed based on number of CPU cores.
• Has some stability issues with high CPU counts.

FiberHMM v1.0

An updated, streamlined version of FiberHMM to replace the older snapshot posted yesterday.

FiberHMM outdated snapshot

A snapshot of FiberHMM as used in the preprint https://www.biorxiv.org/content/10.1101/2023.12.22.573133v1

FiberHMM outdated snapshot

A snapshot of FiberHMM as used in the preprint https://www.biorxiv.org/content/10.1101/2023.12.22.573133v1