inst/testScripts/bwa/11.bwa,index,level1.R

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

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library("aroma.seq");

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# Session information
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# Assert that BWA is available
pathname <- findBWA();
printf("BWA executable: %s\n", pathname);

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Indexing a reference genome
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path <- "annotationData/organisms/Lambda_phage";
pathnameFA <- file.path(path, "lambda_virus.fa");
pathnameFA <- Arguments$getReadablePathname(pathnameFA);
prefix <- bwaIndexPrefix(pathnameFA, method="bwtsw");
prefix <- Arguments$getWritablePathname(prefix) ## TAT addition; skip the mustNotExist=T
res <- systemBWA("index", a="is", p=prefix, pathnameFA, verbose=TRUE);
print(res);

files <- list.files(path=getParent(prefix));
print(files);


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