Files in SICtools
Find SNV/Indel differences between two bam files with near relationship

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/SICtools-internal.R R/indelDiff.R R/snpDiff.R
build
build/vignette.rds
inst
inst/doc
inst/doc/SICtools.R inst/doc/SICtools.Rmd inst/doc/SICtools.pdf
inst/extdata
inst/extdata/example.ref.fasta
inst/extdata/example.ref.fasta.fai
inst/extdata/example1.bam
inst/extdata/example1.bam.bai
inst/extdata/example2.bam
inst/extdata/example2.bam.bai
inst/unitTests
inst/unitTests/runTests.R inst/unitTests/test_indelDiff.R inst/unitTests/test_snpDiff.R
man
man/SICtools-package.Rd man/indelDiff.Rd man/snpDiff.Rd
src
src/AUTHORS
src/COPYING
src/ChangeLog.old
src/INSTALL
src/Makefile
src/Makefile.mingw
src/NEWS
src/bam.c
src/bam.h
src/bam2bcf.c
src/bam2bcf.h
src/bam2bcf_indel.c
src/bam2depth.c
src/bam_aux.c
src/bam_cat.c
src/bam_color.c
src/bam_endian.h
src/bam_import.c
src/bam_index.c
src/bam_lpileup.c
src/bam_mate.c
src/bam_md.c
src/bam_pileup.c
src/bam_plcmd.c
src/bam_reheader.c
src/bam_rmdup.c
src/bam_rmdupse.c
src/bam_sort.c
src/bam_stat.c
src/bam_tview.c
src/bam_tview.h
src/bam_tview_curses.c
src/bam_tview_html.c
src/bamshuf.c
src/bamtk.c
src/bcftools
src/bcftools/Makefile
src/bcftools/README
src/bcftools/bcf.c
src/bcftools/bcf.h
src/bcftools/bcf.tex
src/bcftools/bcf2qcall.c
src/bcftools/bcfutils.c
src/bcftools/call1.c
src/bcftools/em.c
src/bcftools/fet.c
src/bcftools/index.c
src/bcftools/kfunc.c
src/bcftools/kmin.c
src/bcftools/kmin.h
src/bcftools/main.c
src/bcftools/mut.c
src/bcftools/prob1.c
src/bcftools/prob1.h
src/bcftools/vcf.c
src/bcftools/vcfutils.pl
src/bedcov.c
src/bedidx.c
src/bgzf.c
src/bgzf.h
src/bgzip.c
src/chk_indel.c
src/cut_target.c
src/errmod.c
src/errmod.h
src/examples
src/examples/00README.txt
src/examples/Makefile
src/examples/bam2bed.c
src/examples/calDepth.c
src/examples/chk_indel.c
src/examples/ex1.fa
src/examples/ex1.sam.gz
src/examples/toy.fa
src/examples/toy.sam
src/faidx.c
src/faidx.h
src/install.libs.R
src/kaln.c
src/kaln.h
src/khash.h
src/klist.h
src/knetfile.c
src/knetfile.h
src/kprobaln.c
src/kprobaln.h
src/kseq.h
src/ksort.h
src/kstring.c
src/kstring.h
src/misc
src/misc/HmmGlocal.java
src/misc/Makefile
src/misc/ace2sam.c
src/misc/bamcheck.c
src/misc/blast2sam.pl
src/misc/bowtie2sam.pl
src/misc/export2sam.pl
src/misc/interpolate_sam.pl
src/misc/maq2sam.c
src/misc/md5.c
src/misc/md5.h
src/misc/md5fa.c
src/misc/novo2sam.pl
src/misc/plot-bamcheck
src/misc/psl2sam.pl
src/misc/r2plot.lua
src/misc/sam2vcf.pl
src/misc/samtools.pl
src/misc/soap2sam.pl
src/misc/varfilter.py
src/misc/vcfutils.lua
src/misc/wgsim.c
src/misc/wgsim_eval.pl
src/misc/zoom2sam.pl
src/padding.c
src/phase.c
src/razf.c
src/razf.h
src/razip.c
src/sam.c
src/sam.h
src/sam_header.c
src/sam_header.h
src/sam_view.c
src/sample.c
src/sample.h
src/samtools.1
src/win32
src/win32/xcurses.h
src/win32/zconf.h
src/win32/zlib.h
tests
tests/runTests.R
vignettes
vignettes/SICtools.Rmd
SICtools documentation built on May 31, 2017, 11:10 a.m.