- clippy
 - clippy
 - clippy
 - unused
 - cli
 - cli
 - cli
 - update ctcf definition
 - prep for bump
 - pyft bump
 - hide m5c #54
 - hide m5c #54
 - extend docs #54
 - cargo dist

### New Features

 - skip empty regions
 - skip empty regions
 - add a ddda to m6a converter
 - switch to generic cpu
 - switch to generic cpu
 - add ont fire heuristic test data and cli improments
 - add ont fire heuristic
 - add ont fire heuristic
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - starting the book
 - add options motif_span
 - more input bam functions
 - more input bam functions
 - InputBam now can make a template for an output bam
 - InputBam now can make a template for an output bam
 - allow the complexity of the pipeup to be adjusted
 - pileup is now useable
 - pileup is now useable
 - pileup is now useable
 - add a pyft way to iterate over a bam file one read at a time.
 - allow fire opts to be read from env vars.
 - inital fibertools pileup is complete
 - inital fibertools pileup is complete
 - inital fibertools pileup is complete

### Bug Fixes

 - make footprint u16 number of modules consistent
 - use bit flag filter
 - use min ml score in pileup
 - check for end of chrom
 - missing final base in pileup region
 - clean up cli interactions with pileup
 - clean up cli interactions with pileup
 - clean up cli interactions with pileup
 - clean up cli interactions with pileup
 - clean up cli interactions with pileup
 - clean up cli interactions with pileup
 - clean up cli interactions with pileup
 - clean up cli interactions with pileup
 - clean up cli interactions with pileup
 - fix label on FIRE vs LINKER for decorator tracks
 - keep footprint code
 - skip sites with zero spanning reads
 - skip sites with zero spanning reads
 - pileup thread error
 - pileup thread error
 - add target names to pyft
 - add target names to pyft
 - add target names to pyft
 - add new check to avoid a new failure on unaligned bams
 - py-ft build
 - py-ft build

### Other

 - removing unneeded nesting
 - Major change to the cli and adding a filtering tools that works like samtools view \-F
 - why are the revio tests failing?

### Refactor

 - move some tests
 - update for fibertools refactor
 - move some complexity into utils
 - move some complexity into utils
 - move some complexity into utils
 - move some complexity into utils
 - move some complexity into utils
 - move the running of subcommands into a submodule called subcommands
 - move the running of subcommands into a submodule called subcommands
 - Breakout subcommands opts into different files
 - Make the inputbam function a utility and add a FiberFilter structure that can be used to filter the input bam and therefore the output

### Commit Statistics

 - 137 commits contributed to the release over the course of 112 calendar days.
 - 131 days passed between releases.
 - 115 commits were understood as [conventional](https://www.conventionalcommits.org).
 - 0 issues like '(#ID)' were seen in commit messages

### Commit Details

 * **Uncategorized**
    - Make footprint u16 number of modules consistent (489f343)
    - Clippy (bebf51d)
    - Clippy (3eb0bf4)
    - Clippy (5195a1d)
    - Outline where Shane may want to add things for our new filter expression ideas (a60ee3e)
    - Move some tests (571d4a3)
    - Update for fibertools refactor (2fa2518)
    - Move some complexity into utils (4796b8b)
    - Move some complexity into utils (9d54591)
    - Move some complexity into utils (6d590e3)
    - Move some complexity into utils (10c4210)
    - Move some complexity into utils (d4e3977)
    - Removing unneeded nesting (9a92b67)
    - Move the running of subcommands into a submodule called subcommands (b3bcece)
    - Move the running of subcommands into a submodule called subcommands (c838410)
    - Breakout subcommands opts into different files (1751215)
    - Make the inputbam function a utility and add a FiberFilter structure that can be used to filter the input bam and therefore the output (f8f2f43)
    - Use bit flag filter (a959126)
    - Use min ml score in pileup (0d035ce)
    - Check for end of chrom (69942fe)
    - Skip empty regions (e088980)
    - Skip empty regions (1e75fb4)
    - Missing final base in pileup region (bff5459)
    - Get ucsc tools into conda (2b9d282)
    - Add a ddda to m6a converter (506ba76)
    - Clean up cli interactions with pileup (43941c3)
    - Clean up cli interactions with pileup (d7f35ae)
    - Clean up cli interactions with pileup (cfb6feb)
    - Clean up cli interactions with pileup (7e4decf)
    - Clean up cli interactions with pileup (bf5d6dc)
    - Clean up cli interactions with pileup (e8da753)
    - Clean up cli interactions with pileup (f2adf3c)
    - Clean up cli interactions with pileup (c5004b9)
    - Clean up cli interactions with pileup (e574b06)
    - Fix label on FIRE vs LINKER for decorator tracks (c92a4d4)
    - Keep footprint code (7546c09)
    - Skip sites with zero spanning reads (c87e12e)
    - Skip sites with zero spanning reads (92284b3)
    - Switch to generic cpu (f732064)
    - Switch to generic cpu (86087ec)
    - Add ont fire heuristic test data and cli improments (274ce9e)
    - Add ont fire heuristic (5d42c01)
    - Add ont fire heuristic (6ab1edb)
    - Move the book to its own repo (f298692)
    - Move the book to its own repo (7c2f224)
    - Starting the book (be05cbe)
    - Starting the book (55208f7)
    - Starting the book (e92de35)
    - Starting the book (cf03b1d)
    - Starting the book (46b418a)
    - Starting the book (9525257)
    - Starting the book (8e609ee)
    - Starting the book (b9c7a3b)
    - Starting the book (8ab2992)
    - Starting the book (3cfd780)
    - Starting the book (752d225)
    - Starting the book (1a3e75b)
    - Starting the book (ab75af5)
    - Pileup thread error (570d3f6)
    - Pileup thread error (7bebe18)
    - Starting the book (e7800cf)
    - Starting the book (9120ab7)
    - Starting the book (c37dec5)
    - Starting the book (c1b2af0)
    - Starting the book (2d02305)
    - Starting the book (b576fca)
    - Starting the book (d09fd87)
    - Starting the book (99056a4)
    - Starting the book (a72b390)
    - Starting the book (70323b0)
    - Starting the book (04dd93d)
    - Starting the book (0471806)
    - Starting the book (4b6006b)
    - Starting the book (7fe6971)
    - Starting the book (4fb0e40)
    - Starting the book (bc8558a)
    - Starting the book (eb7f370)
    - Starting the book (f8a7592)
    - Starting the book (01a3e8a)
    - Starting the book (3b4f9c9)
    - Starting the book (9be4ca0)
    - Starting the book (c5d30a9)
    - Starting the book (27e5dc2)
    - Starting the book (3379e16)
    - Starting the book (3e98f2d)
    - Starting the book (b8ffdd8)
    - Unused (7c7abcb)
    - Cli (7342219)
    - Cli (1a4df89)
    - Cli (23f7c70)
    - Add options motif_span (34138f6)
    - Update ctcf definition (b0bdc44)
    - More input bam functions (1caf278)
    - More input bam functions (5fa8f29)
    - InputBam now can make a template for an output bam (2465fe7)
    - InputBam now can make a template for an output bam (01bd5f7)
    - Test a fix for doc build error (0a2b7ee)
    - Small (5ad6b6b)
    - Small (6fff5e9)
    - Small (ec0c5b6)
    - Small (f5bffa1)
    - Small (0113df4)
    - Small (d583bdb)
    - Small (ac32395)
    - Test a fix for doc build error (024f24f)
    - Major change to the cli and adding a filtering tools that works like samtools view \-F (8d9a1b4)
    - Test a fix for doc build error (1aa875c)
    - Test a fix for doc build error (15274ea)
    - Test a fix for doc build error (7a190a1)
    - Add target names to pyft (fbc50c5)
    - Add target names to pyft (370ea24)
    - Add target names to pyft (7357ab0)
    - Test a fix for doc build error (112c581)
    - Test a fix for doc build error (5714739)
    - Test a fix for doc build error (4389dc5)
    - Test a fix for doc build error (20a16d2)
    - Add new check to avoid a new failure on unaligned bams (7ec0651)
    - Why are the revio tests failing? (c887abc)
    - Allow the complexity of the pipeup to be adjusted (16c18ee)
    - Prep for bump (95d5ddb)
    - Pileup is now useable (844f2a2)
    - Pileup is now useable (f709630)
    - Pileup is now useable (9a2530a)
    - Pyft bump (49b5e83)
    - Add a pyft way to iterate over a bam file one read at a time. (831e5a0)
    - Hide m5c #54 (956474d)
    - Hide m5c #54 (b5dfd1e)
    - Extend docs #54 (6260d39)
    - Allow fire opts to be read from env vars. (3fea667)
    - Clean (8b6a1ac)
    - Inital fibertools pileup is complete (b4ac782)
    - Inital fibertools pileup is complete (20e4ef6)
    - Inital fibertools pileup is complete (f512b19)
    - Py-ft build (9c4dea1)
    - Py-ft build (714a8dc)
    - Cargo dist (3ca6260)
    - Start work on making a fire track (351cb91)