inst/testScripts/complete/hg19/21.FastaReferenceFile,BWA.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

############################################################################
#
############################################################################
library("aroma.seq");

organism <- "Homo_sapiens";

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Indexing a reference genome
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
path <- file.path("annotationData", "organisms", organism);
filename <- "human_g1k_v37.fasta";
fa <- FastaReferenceFile(filename, path=path);
print(fa);


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Build BWA index set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
is <- buildBwaIndexSet(fa, verbose=-10);
print(is);


############################################################################
# HISTORY:
# 2012-09-24
# o Created.
############################################################################