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update changelog 0.2.5 and build docs for 0.2.5
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@ArtRand
ArtRand committed Mar 5, 2024
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12 changes: 12 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,18 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [v0.2.5]
### Fixes
- [extract] Only emit mapped reads when `--region` is provided, but still emit unmapped bases in those reads unless `--mapped-only` is passed.
- [extract] Performance improvement due to better tracking of interval boundaries.
- [repair] Updates the `MN` tag on repaired records.
### Adds
- [dmr, single-site] Refactor `dmr pair` without regions (i.e. single site analysis) to increase performance.
- [dmr, single-site] Add estimated MAP-based p-value to output.
- [all] Allows BED3 input for all options that use `--include-bed`. Strand will be assumed to be BOTH (equivalent to '.').
- [extract] Increases the kmer size limit to 50.


## [v0.2.5-rc2]
### Fixes
- [all] Reads with entirely implicit canonical calls are no longer skipped for "modbase info empty" or similar.
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103 changes: 78 additions & 25 deletions book/src/advanced_usage.md
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Expand Up @@ -9,6 +9,8 @@ modified base information (modBAMs). The various sub-commands and tools availabl

```text
Modkit is a bioinformatics tool for working with modified bases from Oxford Nanopore
Usage: modkit <COMMAND>
Commands:
Expand Down Expand Up @@ -764,8 +766,8 @@ Options:
Hide the progress bar.
--kmer-size <KMER_SIZE>
Set the query and reference k-mer size (if a reference is provided). Maxumum number for
this value is 12.
Set the query and reference k-mer size (if a reference is provided). Maximum number for
this value is 50.
[default: 5]
Expand Down Expand Up @@ -951,19 +953,19 @@ Options:
Canonical base to evaluate. By default, this will be derived from mod codes in ground
truth BED files. For ground truth with only canonical sites and/or ChEBI codes this values
must be set.
[possible values: A, C, G, T]
-q, --filter-quantile <FILTER_QUANTILE>
Filter out modified base calls where the probability of the predicted variant is below
this confidence percentile. For example, 0.1 will filter out the 10% lowest confidence
modification calls.
[default: 0.1]
-t, --threads <THREADS>
Number of threads to use.
[default: 4]
--suppress-progress
Expand Down Expand Up @@ -1153,7 +1155,7 @@ Options:
Print help information (use `-h` for a summary).
```

## pileup-hemi `pair`
## dmr pair
```text
Compare regions in a pair of samples (for example, tumor and normal or control and experiment). A
sample is input as a bgzip pileup bedMethyl (produced by pileup, for example) that has an associated
Expand All @@ -1167,66 +1169,116 @@ Options:
Bgzipped bedMethyl file for the first (usually control) sample. There should be a tabix
index with the same name and .tbi next to this file or the --index-a option must be
provided.
-b <EXP_BED_METHYL>
Bgzipped bedMethyl file for the second (usually experimental) sample. There should be a
tabix index with the same name and .tbi next to this file or the --index-b option must be
provided.
-o, --out-path <OUT_PATH>
Path to file to direct output, optional, no argument will direct output to stdout.
Path to file to direct output, optional, no argument will direct output to stdout
--header
Include header in output.
-r, --regions-bed <REGIONS_BED>
BED file of regions over which to compare methylation levels. Should be tab-separated
(spaces allowed in the "name" column). Requires chrom, chromStart and chromEnd. The Name
column is optional. Strand is currently ignored. When omitted, methylation levels are
compared at each site in the `-a`/`control_bed_methyl` BED file (or optionally, the
`-b`/`exp_bed_methyl` file with the `--use-b` flag.
--use-b
When performing site-level DMR, use the bedMethyl indicated by the -b/exp_bed_methyl
argument to collect bases to score.
compared at each site.
--ref <REFERENCE_FASTA>
Path to reference fasta for the pileup.
Path to reference fasta for used in the pileup/alignment.
-m <MODIFIED_BASES>
Bases to use to calculate DMR, may be multiple. For example, to calculate differentially
methylated regions using only cytosine modifications use --base C.
--log-filepath <LOG_FILEPATH>
File to write logs to, it's recommended to use this option.
-t, --threads <THREADS>
Number of threads to use [default: 4]
Number of threads to use.
[default: 4]
--batch-size <BATCH_SIZE>
Control the batch size. The batch size is the number of regions to load at a time. Each
region will be processed concurrently. Loading more regions at a time will decrease IO to
load data, but will use more memory. Default will be 50% more than the number of threads
assigned.
-k, --mask
Respect soft masking in the reference FASTA.
--suppress-progress
Don't show progress bars.
-f, --force
Force overwrite of output file, if it already exists.
--index-a <INDEX_A>
Path to tabix index associated with -a (--control-bed-methyl) bedMethyl file.
--index-b <INDEX_B>
Path to tabix index associated with -b (--exp-bed-methyl) bedMethyl file.
--missing <HANDLE_MISSING>
How to handle regions found in the `--regions` BED file. quiet => ignore regions that are
not found in the tabix header warn => log (debug) regions that are missing fatal => log
(error) and exit the program when a region is missing. [default: warn] [possible values:
quiet, warn, fail]
(error) and exit the program when a region is missing.
[default: warn]
[possible values: quiet, warn, fail]
--min-valid-coverage <MIN_VALID_COVERAGE>
Minimum valid coverage required to use an entry from a bedMethyl. See the help for pileup
for the specification and description of valid coverage. [default: 0]
for the specification and description of valid coverage.
[default: 0]
--prior <PRIOR> <PRIOR>
Prior distribution for estimating MAP-based p-value. Should be two arguments for alpha and
beta (e.g. 1.0 1.0). See `dmr_scoring_details.md` for additional details on how the metric
is calculated.
--delta <DELTA>
Consider only effect sizes greater than this when calculating the MAP-based p-value.
[default: 0.05]
-N, --n-sample-records <N_SAMPLE_RECORDS>
Sample this many reads when estimating the max coverage thresholds.
[default: 10042]
--max-coverages <MAX_COVERAGES> <MAX_COVERAGES>
Max coverages to enforce when calculating estimated MAP-based p-value.
--cap-coverages
When using replicates, cap coverage to be equal to the maximum coverage for a single
sample. For example, if there are 3 replicates with max_coverage of 30, the total coverage
would normally be 90. Using --cap-coverages will down sample the data to 30X.
-i, --interval-size <INTERVAL_SIZE>
Interval chunk size in base pairs to process concurrently. Smaller interval chunk sizes
will use less memory but incur more overhead.
[default: 100000]
-h, --help
Print help information.
Print help information (use `-h` for a summary).
```

## pileup-hemi
## dmr multi
```text
Compare regions between all pairs of samples (for example a trio sample set or haplotyped trio
sample set). As with `pair` all inputs must be bgzip compressed bedMethyl files with associated
tabix indices. Each sample must be assigned a name. Output is a directory of BED files with the
score column indicating the magnitude of the difference in methylation between the two samples
indicated in the file name. See the online documentation for additional details.
indicated in the file name. See the online documentation for additional details
Usage: modkit dmr multi [OPTIONS] --out-dir <OUT_DIR> --ref <REFERENCE_FASTA>
Usage: modkit dmr multi [OPTIONS] --regions-bed <REGIONS_BED> --out-dir <OUT_DIR> --ref <REFERENCE_FASTA>
Options:
-s, --sample <SAMPLES> <SAMPLES>
Expand All @@ -1239,8 +1291,9 @@ Options:
-r, --regions-bed <REGIONS_BED>
BED file of regions over which to compare methylation levels. Should be tab-separated
(spaces allowed in the "name" column). Requires chrom, chromStart and chromEnd. The Name
column is optional. Strand is currently ignored. When omitted, methylation levels are
compared at each site in common between the two bedMethyl files being compared.
column is optional. Strand is currently ignored.
--header
Include header in output.
-o, --out-dir <OUT_DIR>
Directory to place output DMR results in BED format.
-p, --prefix <PREFIX>
Expand All @@ -1259,7 +1312,7 @@ Options:
--suppress-progress
Don't show progress bars.
-f, --force
Force overwrite of output file, if it already exists
Force overwrite of output file, if it already exists.
--missing <HANDLE_MISSING>
How to handle regions found in the `--regions` BED file. quiet => ignore regions that are
not found in the tabix header warn => log (debug) regions that are missing fatal => log
Expand All @@ -1269,5 +1322,5 @@ Options:
Minimum valid coverage required to use an entry from a bedMethyl. See the help for pileup
for the specification and description of valid coverage. [default: 0]
-h, --help
Print help information
Print help information.
```
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