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annot-tsv
base_mods
bcf-sr
faidx
fastq
fuzz
longrefs
maintainer
mpileup
sam_filter
tabix
auxf#values.sam
auxf#values_java.cram
auxf.fa
auxf.fa.fai
bgziptest.txt
bgziptest.txt.gz
bgziptest.txt.gz.gzi
c1#bounds.sam
c1#clip.sam
c1#noseq.sam
c1#pad1.sam
c1#pad2.sam
c1#pad3.sam
c1#unknown.sam
c1.fa
c1.fa.fai
c2#pad.sam
c2.fa
c2.fa.fai
ce#1.sam
ce#1000.sam
ce#2.sam
ce#5.sam
ce#5b.sam
ce#5b_java.cram
ce#large_seq.sam
ce#supp.sam
ce#tag_depadded.sam
ce#tag_padded.sam
ce#unmap.sam
ce#unmap1.sam
ce#unmap2.sam
ce.fa
ce.fa.fai
colons.bam
colons.bam.bai
compare_sam.pl
cross_validate.sh
emptyfile
fastqs_README.txt
fieldarith.c
fieldarith.sam
formatcols.vcf
formatmissing-out.vcf
formatmissing.vcf
header_syms.pl
hfile.c
hts_endian.c
index.bam.bai
index.bam.csi
index.bcf.csi
index.cram.crai
index.sam
index.sam.gz.bai
index.sam.gz.csi
index.vcf
index.vcf.gz.csi
index.vcf.gz.tbi
index2.sam
index_dos.sam
md#1.sam
md.fa
md.fa.fai
modhdr.expected.vcf
modhdr.vcf.gz
modhdr.vcf.gz.csi
no_hdr_sq_1.bam
no_hdr_sq_1.bam.csi
no_hdr_sq_1.expected.sam
noroundtrip-out.vcf
noroundtrip.vcf
pileup.c
pileup_mod.c
plugins-dlhts.c
range.bam
range.bam.bai
range.cram
range.cram.crai
range.out
realn01.fa
realn01.fa.fai
realn01.sam
realn01_exp-a.sam
realn01_exp-e.sam
realn01_exp.sam
realn02-r.sam
realn02.fa
realn02.fa.fai
realn02.sam
realn02_exp-a.sam
realn02_exp-e.sam
realn02_exp.sam
realn03.fa
realn03.fa.fai
realn03.sam
realn03_exp.sam
sam.c
simple_test_driver.sh
tabix.out
test-bcf-sr.c
test-bcf-sr.pl
test-bcf-translate.c
test-bcf-translate.out
test-bcf_set_variant_type.c
test-logging.pl
test-parse-reg.c
test-regidx.c
test-vcf-api.c
test-vcf-api.out
test-vcf-hdr-in.vcf
test-vcf-hdr.out
test-vcf-sweep.c
test-vcf-sweep.out
test.pl
test_bgzf.c
test_expr.c
test_faidx.c
test_index.c
test_introspection.c
test_kfunc.c
test_kstring.c
test_mod.c
test_realn.c
test_str2int.c
test_time_funcs.c
test_view.c
thrash_threads1.c
thrash_threads2.c
thrash_threads3.c
thrash_threads4.c
thrash_threads5.c
thrash_threads6.c
thrash_threads7.c
thread_pool.md
usepublic.cpp
vcf_meta_meta.vcf
with-shlib.sh
xx#blank.sam
xx#large_aux.sam
xx#large_aux2.sam
xx#large_aux_java.cram
xx#MD.sam
xx#MD2.sam
xx#minimal.sam
xx#pair.sam
xx#repeated.sam
xx#rg.sam
xx#tlen.sam
xx#tlen2.sam
xx#triplet.sam
xx#unsorted.sam
xx.fa
xx.fa.fai
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