dentist.dazzler

Defines bindings and utilities to/for the dazzler commands.

Members

Classes

MaskReaderException
class MaskReaderException

Thrown on failure while reading a Dazzler mask.

Enums

ComputeIntrinsicQVOptions
enum ComputeIntrinsicQVOptions

Options for computeintrinsicqv.

DBdumpOptions
enum DBdumpOptions

Options for DBdump.

DBshowOptions
enum DBshowOptions

Options for DBshow.

DaccordOptions
enum DaccordOptions

Options for daccord.

DalignerOptions
enum DalignerOptions

Options for daligner.

DamapperOptions
enum DamapperOptions

Options for damapper.

Fasta2DazzlerOptions
enum Fasta2DazzlerOptions

Options for fasta2DAM and fasta2DB.

LAdumpOptions
enum LAdumpOptions

Options for LAdump.

LasFilterAlignmentsOptions
enum LasFilterAlignmentsOptions

Options for lasfilteralignments.

ProvideMethod
enum ProvideMethod

Determines how data should be provided in the working directory.

Functions

buildDamFile
string buildDamFile(Range fastaRecords, in string workdir, in string[] dbsplitOptions = [])

Build a .dam file with the given set of FASTA records.

dbSubset
string dbSubset(in string inDbFile, R readIds, in Options options)

Build a new .dam file by using the given subset of reads in inDbFile.

getConsensus
string getConsensus(in string dbFile, in size_t readId, in Options options)
string getConsensus(in string dbFile, in Options options)

Self-dalign dbFile and build consensus using daccord.

getFastaEntries
auto getFastaEntries(in string dbFile, Range recordNumbers, in Options options)

Get the designated set of records in FASTA format. If recordNumbers is empty the whole DB will be converted.

getFastaSequence
auto getFastaSequence(in string dbFile, id_t recordNumber, in string workdir, in id_t cacheSize = 1024)

Get the FASTA sequence of the designated record with prefetching to reduce forks.

getFastaSequences
auto getFastaSequences(in string dbFile, Range recordNumbers, in string workdir)

Get the FASTA sequences of the designated records.

getHiddenDbFiles
auto getHiddenDbFiles(string dbFile)

Return a list of hidden files associated to every .dam/.db file. These files contain the actual data used in all the computation. Thus, we carefully check for their existence.

getMaskFiles
auto getMaskFiles(in string dbFile, in string maskDestination)

Get the hidden files comprising the designated mask.

lasEmpty
bool lasEmpty(in string lasFile, in string dbA, in string workdir)
bool lasEmpty(in string lasFile, in string dbA, in string dbB, in string workdir)

Returns true iff lasFile contains zero parts.

provideDamFileInWorkdir
string provideDamFileInWorkdir(in string dbFile, ProvideMethod provideMethod, in string workdir)

Provide dbFile in workdir.

provideFileInWorkdir
string provideFileInWorkdir(in string file, ProvideMethod provideMethod, in string workdir)

Provide file in workdir.

provideLasFileInWorkdir
string provideLasFileInWorkdir(in string lasFile, ProvideMethod provideMethod, in string workdir)

Provide lasFile in workdir.

readMask
Region[] readMask(in string dbFile, in string maskDestination, in string workdir)

Read the Regions of a Dazzler mask for dbFile.

writeMask
void writeMask(in string dbFile, in string maskDestination, in Region[] regions, in string workdir)

Write the list of regions to a Dazzler mask for dbFile.

Manifest constants

damFileExtension
enum damFileExtension;

Constant holding the .dam file extension.

dbFileExtension
enum dbFileExtension;

Constant holding the .db file extension.

minSequenceLength
enum minSequenceLength;

The Dazzler tools require sequence of a least minSequenceLength base pairs.

Meta

License

Subject to the terms of the MIT license, as written in the included LICENSE file.

Authors

Arne Ludwig <arne.ludwig@posteo.de>