Add B cell receptors.
Add a make target to refresh the reference sequences from RefSeq.
Support multiple organisms.
Define a versionned CDR3 file format and test it before reading in read clonotypes.R
read_clonotypes: do not hardcode column classe, but infer them from the name, that is inferred from the OSC header, or hardcoded as a fallback.
##ProtocolREF = CP-Custom-v1.0
Correct in OSC file
##ParameterValue[qual] = Illumina
Is it correct to have same name for ParameterValue and ColumnName ?
Do we need ?
##NameSpace = genomic_coordinate
- Provide example AB1 and SFF files.
Get good default for CLONOTYPER_REFERENCE and other variables.
Regression tests: make sure that the example data has a sharp sign in the FASTQ sequence (if valid), and compare the number of lines to what is expected.
Support extraction of barcoded reads.
Report the number of V segments found after
Clonotype algebra, like in:
`+.clonotypeList` <- function(X, Y) structure( union(X, Y), class='clonotypeList') `^.clonotypeList` <- function(X, Y) structure( intersect(X, Y), class='clonotypeList') `-.clonotypeList` <- function(X, Y) structure( setdiff(X, Y), class='clonotypeList')