Changelog

import_peaks:
- Can now recognize and read in local/remote file paths passed to ids.
- New subfunction import_peaks_files to support this.
create_trackhub:
- New set of functions to automatically creating UCSC Genome Browser TrackHubs from bigwig, bedGraph, bed, bedGraph files.
New function: bed_to

call_peaks:
- SEACR now implemented!!
- Add parameters as metadata in peak GRanges.
New exported functions:
- merge_bam: Merge multiple BAM files into one.
- pooled_peaks: Pool groups of BAM files and call peaks from them (using either MACSr or SEACR).
- convert_bam: Convert BAM file to any format.
- example_bg_bw
- example_bam
New internal functions:
- report_time
- import_peaks_seacr
- import_peaks_macs
- call_peaks_seacr
- pooled_peaks_seacr/ pooled_peaks_macsr
- make_conda_env
- find_executable_seacr
- add_mcol
- bam_to
Change all call_peaks_method args to simpler –> method.

import_peaks_*: Now handle situations where 0 peaks are called.
import_peaks: Add support to bigBed format.
Switch from BiocParallel to parallel, as the former is extremely buggy and inconsistent.

Removed duplicated files from Google Drive (“(1).R”).
Accidentally hard-coded a GSM ID into process_ids.
Extract supp files from both the project-level GSE ID and sample-level GSM ids.
Figure out why package is unable to find "peaks_metadata_roadmap" unless package is loaded.
Force all rownames to be unique.

Select SnowParam vs. SerialParam depending on OS to avoid issues on Windows.
Fix vignette formatting.
Add error handlers for import.bw on Windows (until someone fixes rtracklayer).
Add error handlers for MACSr on Windows (until it becomes compatible).
Remove import_bigwig_filtered function (not used).

PeakyFinders 0.99.4