590b847e35f144d749c9b6a321728e94 *DESCRIPTION
9030afd6be5ba1b6b8c3599852a9ccc9 *NAMESPACE
f3764b03ab7107beb6e413a8ebd8116c *NEWS
e17db3a3066f3b090786abce99878314 *R/SICtools-internal.R
380862e6e01ac4b2389df036d68dac78 *R/indelDiff.R
1e5daf32709ca03200dde1df285a74ad *R/snpDiff.R
13c4ccdb9dacee7b02c3c430276fe342 *build/vignette.rds
674930e988d41b662912172a5cc4968d *inst/doc/SICtools.R
7dd43f2d8dce987ef2f2615d4451720f *inst/doc/SICtools.Rmd
2c681395927e8c69ecdb2499237721cf *inst/doc/SICtools.pdf
769288375c90e92e26fee254f781cfd9 *inst/extdata/example.ref.fasta
dc4b7c14f5eaa281d6a6c65b13d4dce6 *inst/extdata/example.ref.fasta.fai
2c0b309a33cdc05a72dad31c7d60c35d *inst/extdata/example1.bam
309d2a9724f547103cb970272f439bd8 *inst/extdata/example1.bam.bai
91eda91586f7392b7238d2e807b3a29c *inst/extdata/example2.bam
085d3a5fda9cc369cbfeb6b39126901a *inst/extdata/example2.bam.bai
cc2205d36a74b8811ece552d701a973f *inst/unitTests/runTests.R
2e5d7c1bb95d4f4c6d096cfc6314486f *inst/unitTests/test_indelDiff.R
f47957bff75ef86187d9fe5d97ce8a27 *inst/unitTests/test_snpDiff.R
49e824e6f207c54da5723edf9a327be5 *man/SICtools-package.Rd
6ce66c41c3213ac7fa15bcb026d2209d *man/indelDiff.Rd
380ccdfcf4aaa3526bc51f50c3685497 *man/snpDiff.Rd
4aaba97cc3b5ee20f002719f41c14b0c *src/AUTHORS
42c2c2d6f53566cadf7dc77a7d37d31f *src/COPYING
b0b928ac48f180b96706759eaf4174e6 *src/ChangeLog.old
f3b84bf75d85c2bdfbccd1abc1c14555 *src/INSTALL
517fd7e706b4d007c2daa3c526291e6c *src/Makefile
e7557460013149b696ad066c34af50a0 *src/Makefile.mingw
cd911fb0cd05868ea4e3f18065d79ba5 *src/NEWS
9d038663f44db1fc4ef0a729499356d1 *src/bam.c
f1568e0f089f8caae4d0e4fbe0776835 *src/bam.h
b9b7aae90bc509aa551e4f08c70f0cd8 *src/bam2bcf.c
a2361d2fdafc2c5a7cc94ca138fbe1d3 *src/bam2bcf.h
154b5fe393a34fd1d4205460cd3c62c0 *src/bam2bcf_indel.c
66c7ea9a18b02fec333cb3468952e857 *src/bam2depth.c
5234565753fb7a99c1a2e1f5513077f8 *src/bam_aux.c
2958f378e73a412309226d5001e6fd40 *src/bam_cat.c
b7da4aa98df9fc7bb8eadba085d5c7c3 *src/bam_color.c
aba13a3883d7d117af33a6d8fe8c1ed1 *src/bam_endian.h
25a24acfdf6a8cf1d78f11ccd0c01789 *src/bam_import.c
25f0b3974ae0248bf50b455d5025b1d2 *src/bam_index.c
be75aa61d06c58767d9696a68d663459 *src/bam_lpileup.c
ce3d748d73aa725dac9ceaf3b94def93 *src/bam_mate.c
37099afa1f6a6291a958e9f6b21e75ad *src/bam_md.c
c38bbbd725fce250c08f79a5af924ca5 *src/bam_pileup.c
d47fa157079fcb6c852070c5407585ee *src/bam_plcmd.c
8bbe7f95da18f2691baf4c18cbcbd4ca *src/bam_reheader.c
36155457c510fdb9fa264acf6a8e612b *src/bam_rmdup.c
c4363c8093fcf3b7c23e306a24274ac6 *src/bam_rmdupse.c
068a317e93a8866c1fc675850763eea7 *src/bam_sort.c
1c49400b1ba823a20bdc803a8ad4e6eb *src/bam_stat.c
a1dad44992edd65eb00516c398ec0309 *src/bam_tview.c
20e4a715891f64d3d720168e81953fed *src/bam_tview.h
a9a6e5e6c2a32cd7274c3786085742e4 *src/bam_tview_curses.c
3cb3e6adcdafcd8f2c2347bed20a5365 *src/bam_tview_html.c
a8ca3b22c9edd272c79227055d163677 *src/bamshuf.c
4c92466441eacb2a0505d8cfbb689685 *src/bamtk.c
73ddaca1ac376496757f69f095eeac2a *src/bcftools/Makefile
7d45e246ae3e0a0c4d4c69a2fd61d514 *src/bcftools/README
eea99ba89b5c2df5f878af07897cb3ee *src/bcftools/bcf.c
613fc63007d9a00f264af2666fea9a04 *src/bcftools/bcf.h
2757ae4e4d844a33ad0c4b677885a7f0 *src/bcftools/bcf.tex
15dc29419474f9891950988afcd236dc *src/bcftools/bcf2qcall.c
d8306661e18297606aeec73579925d8c *src/bcftools/bcfutils.c
f76426f70dc0d0fe5ad38c0874d07159 *src/bcftools/call1.c
5654c83c225334964e790a9ff2bb5516 *src/bcftools/em.c
6603ff8ca0e883aecfd25dad50f574b4 *src/bcftools/fet.c
916221c96788fb9a98993142ddec34fa *src/bcftools/index.c
8d6964dda3e85f705dbd9bb3b576572b *src/bcftools/kfunc.c
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377808508da7161674b6ca41e52c098d *src/bcftools/kmin.h
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91e3e918b37ab30b09ba46ed20bb9d06 *src/bcftools/mut.c
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9b250355a7de8ba49adb8a3a2db23770 *src/bcftools/prob1.h
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986a6a216e189ad4c32ce8303873fc48 *src/bedidx.c
a9bc587bd3d0edc5f73c82a3d7557a88 *src/bgzf.c
abd042e94b527d534410175167a07e4a *src/bgzf.h
c7c2d325021f724cf1a2e0f784ee1181 *src/bgzip.c
6b354d1d066bdffddad2a99d84faaeb0 *src/chk_indel.c
1f0a6142348a115ba91cb5348864eac8 *src/cut_target.c
413bbbfa1f2ad48cfe73a7a2af58e57b *src/errmod.c
599d15d91fbc8844fff563916f79f047 *src/errmod.h
3f063eac902c5c56cf2e14ce7241db0a *src/examples/00README.txt
eb672f020558162b10b1f0744dfe99a9 *src/examples/Makefile
81bcc8628654f1eccdbfb5c5f5fdcff1 *src/examples/bam2bed.c
93a012b8ca4dc86fec54af54620b0428 *src/examples/calDepth.c
6b354d1d066bdffddad2a99d84faaeb0 *src/examples/chk_indel.c
2be5bfebdd7764be3af95881ddcc1471 *src/examples/ex1.fa
bfe3074489c68daa9e68a598a84eba03 *src/examples/ex1.sam.gz
64b4b81d8c81d20e11f6aa4e829de01b *src/examples/toy.fa
403ef5f9375e1b41576ef59d3d4922b6 *src/examples/toy.sam
fddded74559217ac14f5236672ea1f67 *src/faidx.c
060c5e036ec8bd44ec5e25549a1e160f *src/faidx.h
07c4252cc3313943cb5285a81b409651 *src/install.libs.R
9f37d8409efd47f15b073b4f019650f3 *src/kaln.c
4c3a3f5ca4f46048f1349aa507e3da81 *src/kaln.h
827428496eca8cc4aa8edd431e884f29 *src/khash.h
0e7522f90ff25602e3dd196a016a5a92 *src/klist.h
71d626516dd76f8fd0fbf954dacea8f6 *src/knetfile.c
02a159fe029305ded4f9d628514dcbca *src/knetfile.h
f859e10af08464ce40aa1ca587bf39fe *src/kprobaln.c
93e492050e605b4b77ee0d0971baf634 *src/kprobaln.h
89e7b91e8dd04627d7ed7833322e8ce9 *src/kseq.h
0de2476fe1b8cb18952ee5b2f81d1540 *src/ksort.h
6b1b42bbbbe56cdd2bdec966f4fbc3e7 *src/kstring.c
e6fa98213a711d4a816a9c35a0a90bdb *src/kstring.h
39e79bb8df243a9a2fc704d92a25b0eb *src/misc/HmmGlocal.java
23e4318980642b2328bd829c5ff6e49b *src/misc/Makefile
9e2b6b46e2ff9fe897fc5f35d8fc906e *src/misc/ace2sam.c
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2e926626064e3389d0358ba96567dea4 *src/misc/export2sam.pl
8eb666744d9931fe7937ad9460d81e0f *src/misc/interpolate_sam.pl
a24586a1449dee77f863b3b37946cbb5 *src/misc/maq2sam.c
07c38b3634d606e5668159e5f475c808 *src/misc/md5.c
e89082b9addd5c27b02ef7e7cc959855 *src/misc/md5.h
4d1a2a6cbc506db6a5ef3b989be0cd1d *src/misc/md5fa.c
703dc98f587510abc4186cb8dc8ad0fe *src/misc/novo2sam.pl
75b5b6e1d2c8ea418c47fa9913f49510 *src/misc/plot-bamcheck
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f4c864567e3383b6ccc12d10faab0886 *src/misc/sam2vcf.pl
1b3f85e26ba0a6e6376069b4f3c1c64e *src/misc/samtools.pl
78460239b3f75bdd24bd03e0fa3437b7 *src/misc/soap2sam.pl
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e926e7fc967bb834e30aecb2889393c4 *src/misc/wgsim.c
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4e811f7eb7d31d182b32aed957ed7231 *src/misc/zoom2sam.pl
570977713b2082bb0c8da0423e97cf16 *src/padding.c
ff5c132a9bfbd32966a2a48ba7879501 *src/phase.c
29247c24d6ffa5920dbe8af1c9f89f49 *src/razf.c
afd2968a10cbf237b0dc3ce0e39a0e7c *src/razf.h
90366acb8b4df440b5c7263d05f74ad6 *src/razip.c
15cd6dfec915afbdb72b8cfa84880cc9 *src/sam.c
3e155e8b01994c3c81f139dfa711bc03 *src/sam.h
2221b3b7a008f9727db749ced29a5dce *src/sam_header.c
b06fd42b19dce6166bbd14057b263a9d *src/sam_header.h
1554445bf6eeb6bab8b37146b15d1903 *src/sam_view.c
79a07dbe2790dee36b88fc2f116aacbe *src/sample.c
feb2c2e1cd4c84e7053a8267173c98a2 *src/sample.h
33840e1803e463d7923672163cc4a459 *src/samtools.1
e8bc0b6a35f2e8f447f484516a6fd0ad *src/win32/xcurses.h
d0b5d7082e4506c4f500d073fde64911 *src/win32/zconf.h
9c4b84aff68aa55f2e9bf70481b94333 *src/win32/zlib.h
cc2205d36a74b8811ece552d701a973f *tests/runTests.R
7dd43f2d8dce987ef2f2615d4451720f *vignettes/SICtools.Rmd
