pub enum Commands {
Show 14 variants
Stats {
bam: String,
qbed: bool,
paf: bool,
},
BedLength {
bed: String,
readable: bool,
column: Option<u8>,
},
Filter {
paf: String,
paired_len: u64,
aln: u64,
query: u64,
},
Invert {
paf: String,
},
Liftover {
paf: String,
bed: String,
qbed: bool,
largest: bool,
},
TrimPaf {
paf: String,
match_score: i32,
diff_score: i32,
indel_score: i32,
remove_contained: bool,
},
Orient {
paf: String,
scaffold: bool,
insert: u64,
},
BreakPaf {
paf: String,
max_size: u32,
},
PafToSam {
paf: String,
fasta: Option<String>,
},
FastxSplit {
fastx: Vec<String>,
},
GetFasta {
fasta: String,
bed: String,
strand: bool,
name: bool,
},
Nucfreq {
bam: String,
region: Option<String>,
bed: Option<String>,
small: bool,
},
Repeat {
fasta: String,
min: usize,
},
Suns {
fasta: String,
kmer_size: usize,
max_size: usize,
validate: bool,
},
}
Expand description
This structure contains all the subcommands for rustybam and their help descriptions.
Because of naming conventions for rust enums the commands names have
different capitalization than on the command line.
For example, the Liftover
enum is invoked using rustybam liftover
and the TrimPaf
command with rustybam trim-paf
.
Variants
Stats
Fields
bam: String
Input sam/bam/cram/file.
qbed: bool
Print query coordinates first
paf: bool
Specify that the input is paf format, (must have cg tag with extended cigar).
Get percent identity stats from a sam/bam/cram or PAF. Requires =/X operations in the CIGAR string!
output column descriptions:
perID_by_matches is calculated as:
matches / (matches + mismatches)
perID_by_events is calculated as:
matches / (matches + mismatches + insertion events + deletion events)
perID_by_all is calculated as:
matches / (matches + mismatches + insertion bases + deletion bases)
BedLength
Count the number of bases in a bed file.
Filter
Fields
paf: String
PAF file from minimap2 or unimap. Must have the cg tag, and n matches will be zero unless the cigar uses =X.
paired_len: u64
Minimum number of aligned bases across all alignments between a target and query in order to keep those records.
aln: u64
Minimum alignment length.
query: u64
Minimum query length.
Filter PAF records in various ways.
Invert
Fields
paf: String
PAF file from minimap2 or unimap. Must have the cg tag, and n matches will be zero unless the cigar uses =X.
Invert the target and query sequences in a PAF along with the CIGAR string.
Liftover
Fields
paf: String
PAF file from minimap2 or unimap run with -c and –eqx [i.e. the PAF file must have the cg tag and use extended CIGAR opts (=/X)].
bed: String
BED file of reference regions to liftover to the query.
qbed: bool
Specifies that the BED file contains query coordinates to be lifted onto the reference (reverses direction of liftover).
Note, that this will make the query in the input PAF
the target in the output PAF
.
largest: bool
If multiple records overlap the same region in the
Liftover target sequence coordinates onto query sequence using a PAF.
This is a function for lifting over coordinates from a reference (paftools.js sam2paf
to convert SAM data to PAF format).
The returned file is a PAF file that is trimmed to the regions in the bed file. Even the cigar in the returned PAF file is trimmed so it can be used downstream! Additionally, a tag with the format id:Z:<>
is added to the PAF where <>
is either the 4th column of the input bed file or if not present chr_start_end
.
TrimPaf
Fields
paf: String
PAF file from minimap2 or unimap. Must have the cg tag, and n matches will be zero unless the cigar uses =X.
match_score: i32
Value added for a matching base.
diff_score: i32
Value subtracted for a mismatching base.
indel_score: i32
Value subtracted for an insertion or deletion.
remove_contained: bool
Remove contained alignments as well as overlaps.
Trim PAF records that overlap in query sequence to find and optimal splitting point using dynamic programing.
Note, this can be combined with rb invert
to also trim the target sequence.
This idea is to mimic some of the trimming that happens in PAV to improve breakpoint detection. Starts with the largest overlap and iterates until no query overlaps remain.
Orient
Fields
paf: String
PAF file from minimap2 or unimap. Must have the cg tag, and n matches will be zero unless the cigar uses =X.
scaffold: bool
Generate ~1 query per target that scaffolds together all the records that map to that target sequence.
The order of the scaffold will be determined by the average target position across all the queries, and the name of the new scaffold will be.
insert: u64
Space to add between records.
Orient paf records so that most of the bases are in the forward direction.
Optionally scaffold the queriers so that there is one query per target.
BreakPaf
Fields
paf: String
PAF file from minimap2 or unimap. Must have the cg tag, and n matches will be zero unless the cigar uses =X.
max_size: u32
Maximum indel size to keep in the paf.
Break PAF records with large indels into multiple records (useful for SafFire).
PafToSam
Fields
paf: String
PAF file from minimap2 or unimap. Must have a CIGAR tag.
Convert a PAF file into a SAM file. Warning, all alignments will be marked as primary!
FastxSplit
Splits fastx from stdin into multiple files.
Specifically it reads fastx format (fastq, fasta, or mixed) from stdin and divides the records across multiple output files. Output files can be compressed by adding .gz
, and the input can also be compressed or uncompressed.
GetFasta
Fields
fasta: String
Fasta file to extract sequences from.
bed: String
BED file of regions to extract.
strand: bool
Reverse complement the sequence if the strand is “-”.
name: bool
Add the name (4th column) to the header of the fasta output.
Mimic bedtools getfasta but allow for bgzip in both bed and fasta inputs.
Nucfreq
Fields
bam: String
Input sam/bam/cram/file.
bed: Option<String>
Print nucfreq info from regions in the bed file output is optionally tagged using the 4th column.
small: bool
Smaller output format.
Get the frequencies of each bp at each position.
Repeat
Report the longest exact repeat length at every position in a fasta.
Suns
Fields
fasta: String
Input fasta file with the genome.
kmer_size: usize
The size of the required unique kmer.
max_size: usize
The maximum size SUN interval to report.
validate: bool
Confirm all the SUNs (very slow) only for debugging.
Extract the intervals in a genome (fasta) that are made up of SUNs.
Trait Implementations
sourceimpl FromArgMatches for Commands
impl FromArgMatches for Commands
sourcefn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>
fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>
sourcefn from_arg_matches_mut(
__clap_arg_matches: &mut ArgMatches
) -> Result<Self, Error>
fn from_arg_matches_mut(
__clap_arg_matches: &mut ArgMatches
) -> Result<Self, Error>
sourcefn update_from_arg_matches(
&mut self,
__clap_arg_matches: &ArgMatches
) -> Result<(), Error>
fn update_from_arg_matches(
&mut self,
__clap_arg_matches: &ArgMatches
) -> Result<(), Error>
ArgMatches
to self
.sourcefn update_from_arg_matches_mut<'b>(
&mut self,
__clap_arg_matches: &mut ArgMatches
) -> Result<(), Error>
fn update_from_arg_matches_mut<'b>(
&mut self,
__clap_arg_matches: &mut ArgMatches
) -> Result<(), Error>
ArgMatches
to self
.sourceimpl Subcommand for Commands
impl Subcommand for Commands
sourcefn augment_subcommands<'b>(__clap_app: Command<'b>) -> Command<'b>
fn augment_subcommands<'b>(__clap_app: Command<'b>) -> Command<'b>
sourcefn augment_subcommands_for_update<'b>(__clap_app: Command<'b>) -> Command<'b>
fn augment_subcommands_for_update<'b>(__clap_app: Command<'b>) -> Command<'b>
sourcefn has_subcommand(__clap_name: &str) -> bool
fn has_subcommand(__clap_name: &str) -> bool
Self
can parse a specific subcommandAuto Trait Implementations
impl RefUnwindSafe for Commands
impl Send for Commands
impl Sync for Commands
impl Unpin for Commands
impl UnwindSafe for Commands
Blanket Implementations
sourceimpl<T> BorrowMut<T> for Twhere
T: ?Sized,
impl<T> BorrowMut<T> for Twhere
T: ?Sized,
const: unstable · sourcefn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
impl<T> Pointable for T
impl<T> Pointable for T
impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
fn to_subset(&self) -> Option<SS>
fn to_subset(&self) -> Option<SS>
self
from the equivalent element of its
superset. Read morefn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
self
is actually part of its subset T
(and can be converted to it).fn to_subset_unchecked(&self) -> SS
fn to_subset_unchecked(&self) -> SS
self.to_subset
but without any property checks. Always succeeds.fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
self
to the equivalent element of its superset.