Module dentist.common
This package holds common code for the DENTIST algorithm.
Functions
| Name | Description |
dentistEnforce(value, msg, payload, file, line)
|
Enforces that the given value is true. If the given value is false, a
DentistException is thrown.
|
to(alignmentChain)
|
Returns the alignment region of alignmentChain.
|
toInterval(alignment)
|
Get the interval that the alignment covers. This method does returns a
single interval from the first to the last matching base pair. It takes
complementary alignments into account when an interval on contigB is
requested
|
Classes
| Name | Description |
DentistException
|
Thrown if some runtime error in the DENTIST algorithm occurs.
|
Structs
| Name | Description |
OutputCoordinate
|
A point on the output assembly. This is used in the translate-coords
command.
|
Manifest constants
| Name | Type | Description |
isTesting
|
|
True iff building with testing commands.
|
testingOnly
|
|
Evaluate to value if building with testing command;
otherwise to typeof(value).init.
|
Aliases
| Name | Type | Description |
ReadInterval
|
Region!(ulong,ulong,"readId",0L)
|
A region, interval or point of the reference/read.
|
ReadPoint
|
Region!(ulong,ulong,"readId",0L)
|
A region, interval or point of the reference/read.
|
ReadRegion
|
Region!(ulong,ulong,"readId",0L)
|
A region, interval or point of the reference/read.
|
ReferenceInterval
|
Region!(ulong,ulong,"contigId",0L)
|
A region, interval or point of the reference/read.
|
ReferencePoint
|
Region!(ulong,ulong,"contigId",0L)
|
A region, interval or point of the reference/read.
|
ReferenceRegion
|
Region!(ulong,ulong,"contigId",0L)
|
A region, interval or point of the reference/read.
|