Files in mskilab/bamUtils
Utility functions for manipulating BAMs
.Rbuildignore
.github/.gitignore
.github/workflows/check-release.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
NAMESPACE
R/bamUtils.R
README.md
bamUtils-manual.pdf
data-raw/create_example_bam.sh
docs/authors.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
inst/extdata/HCC1143.final.subset.bam
inst/extdata/HCC1143.final.subset.bam.bai
inst/extdata/bam_noindex.bam
inst/extdata/chr1_human_g1k_v37_decoy.subset.fasta
inst/extdata/chrom1.vcf
inst/extdata/smallA4AD_BL.bam
inst/extdata/smallA4AD_BL.bam.bai
inst/extdata/smallA4AD_tum.bam
inst/extdata/smallA4AD_tum.bam.bai
inst/extdata/smallHCC1143BL.bam
inst/extdata/smallHCC1143BL.bam.bai
inst/extdata/smallHCC1143BL.filtered.MD.bam
inst/extdata/smallHCC1143BL.filtered.MD.bam.bai
inst/extdata/snv.annotated.A4AD.maf
man/bam.cov.gr.Rd
man/bam.cov.tile.Rd
man/bamflag.Rd
man/bamorcram.Rd
man/bamtag.Rd
man/chunk.Rd
man/count.clips.Rd
man/countCigar.Rd
man/get.mate.gr.Rd
man/get.pairs.grl.Rd
man/is.paired.end.Rd
man/mafcount.Rd
man/read.bam.Rd
man/splice.cigar.Rd
man/varbase.Rd
man/varcount.Rd
old.travis.yml
tests/testthat.R
tests/testthat/HCC1143.final.subset.bam
tests/testthat/HCC1143.final.subset.bam.bai
tests/testthat/HCC1143.final.subset.bw
tests/testthat/HCC1143BL.final.percent.bam
tests/testthat/HCC1143BL.final.percent.bam.bai
tests/testthat/bam_noindex.bam
tests/testthat/chr1_human_g1k_v37_decoy.subset.fasta
tests/testthat/chr1_human_g1k_v37_decoy.subset.fasta.fai
tests/testthat/chrom1.vcf
tests/testthat/fake_bam.txt
tests/testthat/foo.vcf
tests/testthat/new_header.vcf
tests/testthat/small.maf
tests/testthat/smallA4AD_BL.bam
tests/testthat/smallA4AD_BL.bam.bai
tests/testthat/smallA4AD_tum.bam
tests/testthat/smallA4AD_tum.bam.bai
tests/testthat/smallHCC1143BL.bam
tests/testthat/smallHCC1143BL.bam.bai
tests/testthat/smallHCC1143BL.filtered.MD.bam
tests/testthat/smallHCC1143BL.filtered.MD.bam.bai
tests/testthat/snv.annotated.A4AD.maf
tests/testthat/test_bamUtils_ops.R
