lib/R/library/Rhtslib/DESCRIPTION lib/R/library/Rhtslib/INDEX lib/R/library/Rhtslib/Meta/Rd.rds lib/R/library/Rhtslib/Meta/features.rds lib/R/library/Rhtslib/Meta/hsearch.rds lib/R/library/Rhtslib/Meta/links.rds lib/R/library/Rhtslib/Meta/nsInfo.rds lib/R/library/Rhtslib/Meta/package.rds lib/R/library/Rhtslib/Meta/vignette.rds lib/R/library/Rhtslib/NAMESPACE lib/R/library/Rhtslib/NEWS lib/R/library/Rhtslib/R/Rhtslib lib/R/library/Rhtslib/R/Rhtslib.rdb lib/R/library/Rhtslib/R/Rhtslib.rdx lib/R/library/Rhtslib/doc/Rhtslib.R lib/R/library/Rhtslib/doc/Rhtslib.Rmd lib/R/library/Rhtslib/doc/Rhtslib.html lib/R/library/Rhtslib/doc/index.html lib/R/library/Rhtslib/help/AnIndex lib/R/library/Rhtslib/help/Rhtslib.rdb lib/R/library/Rhtslib/help/Rhtslib.rdx lib/R/library/Rhtslib/help/aliases.rds lib/R/library/Rhtslib/help/paths.rds lib/R/library/Rhtslib/html/00Index.html lib/R/library/Rhtslib/html/R.css lib/R/library/Rhtslib/include/README lib/R/library/Rhtslib/include/bam_cat.c lib/R/library/Rhtslib/include/bam_plbuf.c lib/R/library/Rhtslib/include/bam_plbuf.h lib/R/library/Rhtslib/include/bam_sort.c lib/R/library/Rhtslib/include/bedidx.c lib/R/library/Rhtslib/include/bedidx.h lib/R/library/Rhtslib/include/htslib/bgzf.h lib/R/library/Rhtslib/include/htslib/cram.h lib/R/library/Rhtslib/include/htslib/faidx.h lib/R/library/Rhtslib/include/htslib/hfile.h lib/R/library/Rhtslib/include/htslib/hts.h lib/R/library/Rhtslib/include/htslib/hts_defs.h lib/R/library/Rhtslib/include/htslib/hts_endian.h lib/R/library/Rhtslib/include/htslib/hts_expr.h lib/R/library/Rhtslib/include/htslib/hts_log.h lib/R/library/Rhtslib/include/htslib/hts_os.h lib/R/library/Rhtslib/include/htslib/kbitset.h lib/R/library/Rhtslib/include/htslib/kfunc.h lib/R/library/Rhtslib/include/htslib/khash.h lib/R/library/Rhtslib/include/htslib/khash_str2int.h lib/R/library/Rhtslib/include/htslib/klist.h lib/R/library/Rhtslib/include/htslib/knetfile.h lib/R/library/Rhtslib/include/htslib/kroundup.h lib/R/library/Rhtslib/include/htslib/kseq.h lib/R/library/Rhtslib/include/htslib/ksort.h lib/R/library/Rhtslib/include/htslib/kstring.h lib/R/library/Rhtslib/include/htslib/regidx.h lib/R/library/Rhtslib/include/htslib/sam.h lib/R/library/Rhtslib/include/htslib/synced_bcf_reader.h lib/R/library/Rhtslib/include/htslib/tbx.h lib/R/library/Rhtslib/include/htslib/thread_pool.h lib/R/library/Rhtslib/include/htslib/vcf.h lib/R/library/Rhtslib/include/htslib/vcf_sweep.h lib/R/library/Rhtslib/include/htslib/vcfutils.h lib/R/library/Rhtslib/include/sam_opts.c lib/R/library/Rhtslib/include/sam_opts.h lib/R/library/Rhtslib/include/sam_utils.c lib/R/library/Rhtslib/include/samtools-1.7-compat.h lib/R/library/Rhtslib/include/samtools.h lib/R/library/Rhtslib/libs/Rhtslib.so lib/R/library/Rhtslib/testdata/auxf#values.sam lib/R/library/Rhtslib/testdata/auxf#values_java.cram lib/R/library/Rhtslib/testdata/auxf.fa lib/R/library/Rhtslib/testdata/auxf.fa.fai lib/R/library/Rhtslib/testdata/c1#bounds.sam lib/R/library/Rhtslib/testdata/c1#clip.sam lib/R/library/Rhtslib/testdata/c1#noseq.sam lib/R/library/Rhtslib/testdata/c1#pad1.sam lib/R/library/Rhtslib/testdata/c1#pad2.sam lib/R/library/Rhtslib/testdata/c1#pad3.sam lib/R/library/Rhtslib/testdata/c1#unknown.sam lib/R/library/Rhtslib/testdata/c1.fa lib/R/library/Rhtslib/testdata/c1.fa.fai lib/R/library/Rhtslib/testdata/c2#pad.sam lib/R/library/Rhtslib/testdata/c2.fa lib/R/library/Rhtslib/testdata/c2.fa.fai lib/R/library/Rhtslib/testdata/ce#1.sam lib/R/library/Rhtslib/testdata/ce#1000.sam lib/R/library/Rhtslib/testdata/ce#2.sam lib/R/library/Rhtslib/testdata/ce#5.sam lib/R/library/Rhtslib/testdata/ce#5b.sam lib/R/library/Rhtslib/testdata/ce#5b_java.cram lib/R/library/Rhtslib/testdata/ce#large_seq.sam lib/R/library/Rhtslib/testdata/ce#supp.sam lib/R/library/Rhtslib/testdata/ce#tag_depadded.sam lib/R/library/Rhtslib/testdata/ce#tag_padded.sam lib/R/library/Rhtslib/testdata/ce#unmap.sam lib/R/library/Rhtslib/testdata/ce#unmap1.sam lib/R/library/Rhtslib/testdata/ce#unmap2.sam lib/R/library/Rhtslib/testdata/ce.fa lib/R/library/Rhtslib/testdata/ce.fa.fai lib/R/library/Rhtslib/testdata/colons.bam lib/R/library/Rhtslib/testdata/faidx.fa lib/R/library/Rhtslib/testdata/fieldarith.sam lib/R/library/Rhtslib/testdata/formatcols.vcf lib/R/library/Rhtslib/testdata/formatmissing-out.vcf lib/R/library/Rhtslib/testdata/formatmissing.vcf lib/R/library/Rhtslib/testdata/index.sam lib/R/library/Rhtslib/testdata/index.vcf lib/R/library/Rhtslib/testdata/index2.sam lib/R/library/Rhtslib/testdata/index_dos.sam lib/R/library/Rhtslib/testdata/md#1.sam lib/R/library/Rhtslib/testdata/md.fa lib/R/library/Rhtslib/testdata/md.fa.fai lib/R/library/Rhtslib/testdata/no_hdr_sq_1.bam lib/R/library/Rhtslib/testdata/no_hdr_sq_1.expected.sam lib/R/library/Rhtslib/testdata/noroundtrip-out.vcf lib/R/library/Rhtslib/testdata/noroundtrip.vcf lib/R/library/Rhtslib/testdata/range.bam lib/R/library/Rhtslib/testdata/range.cram lib/R/library/Rhtslib/testdata/realn01.fa lib/R/library/Rhtslib/testdata/realn01.fa.fai lib/R/library/Rhtslib/testdata/realn01.sam lib/R/library/Rhtslib/testdata/realn01_exp-a.sam lib/R/library/Rhtslib/testdata/realn01_exp-e.sam lib/R/library/Rhtslib/testdata/realn01_exp.sam lib/R/library/Rhtslib/testdata/realn02-r.sam lib/R/library/Rhtslib/testdata/realn02.fa lib/R/library/Rhtslib/testdata/realn02.fa.fai lib/R/library/Rhtslib/testdata/realn02.sam lib/R/library/Rhtslib/testdata/realn02_exp-a.sam lib/R/library/Rhtslib/testdata/realn02_exp-e.sam lib/R/library/Rhtslib/testdata/realn02_exp.sam lib/R/library/Rhtslib/testdata/tabix/bed_file.bed lib/R/library/Rhtslib/testdata/tabix/gff_file.gff lib/R/library/Rhtslib/testdata/tabix/large_chr.vcf lib/R/library/Rhtslib/testdata/tabix/vcf_file.bcf lib/R/library/Rhtslib/testdata/tabix/vcf_file.vcf lib/R/library/Rhtslib/testdata/test-vcf-hdr-in.vcf lib/R/library/Rhtslib/testdata/vcf_meta_meta.vcf lib/R/library/Rhtslib/testdata/xx#MD.sam lib/R/library/Rhtslib/testdata/xx#MD2.sam lib/R/library/Rhtslib/testdata/xx#blank.sam lib/R/library/Rhtslib/testdata/xx#large_aux.sam lib/R/library/Rhtslib/testdata/xx#large_aux2.sam lib/R/library/Rhtslib/testdata/xx#large_aux_java.cram lib/R/library/Rhtslib/testdata/xx#minimal.sam lib/R/library/Rhtslib/testdata/xx#pair.sam lib/R/library/Rhtslib/testdata/xx#repeated.sam lib/R/library/Rhtslib/testdata/xx#rg.sam lib/R/library/Rhtslib/testdata/xx#tlen.sam lib/R/library/Rhtslib/testdata/xx#tlen2.sam lib/R/library/Rhtslib/testdata/xx#triplet.sam lib/R/library/Rhtslib/testdata/xx#unsorted.sam lib/R/library/Rhtslib/testdata/xx.fa lib/R/library/Rhtslib/testdata/xx.fa.fai lib/R/library/Rhtslib/usrlib/libhts.a lib/R/library/Rhtslib/usrlib/libhts.so lib/R/library/Rhtslib/usrlib/libhts.so.2