6988092eaeac9cecdd06d4536d4d0668 *DESCRIPTION
6809a8dbe26f654e576a54304906b8a3 *NAMESPACE
536498905fe2f576a8eee56656e3d26b *R/AllClasses.R
604fd55ffdc0bdd7ff30b661430c3cdd *R/AllGenerics.R
65862a62f9c6b7d532ec6f3602fb624b *R/alignShortReads.R
0afb2dc3cbf012590abb3e8a96f6e0b2 *R/annotateVariants.R
743241a22872480ff406a2e91697162a *R/ava2vcf.R
2dd6f2c8b09a263657e63ec4d86035c6 *R/calculateTiTv.R
e026b8ffa852c53d9d610550490b4457 *R/convertCigar.R
77438afae64a242ea7e2469043dce1d4 *R/coverageOnTarget.R
1992d23bce57006777c67693ba5a6b69 *R/demultiplexReads.R
e455c4bc166f5322b90a35069e9c3544 *R/detectBreakpoints.R
02a81528a1fe6223d48a7869e39e929e *R/filterChimericReads.R
bf30018781b582b4956f5ea2cbcf29d4 *R/filterVariants.R
5faa7ba4cd08ac97f70c7d2640b84ca6 *R/genomeSequencerMIDs.R
6307afdecf891cc09dfd003a6ebcf34f *R/getAlignedReads.R
d46239cd1c799bf0e5f8a3d323a898bb *R/getAminoAbbr.R
1fad44989ada0cd6936f30d9808bb7fd *R/htmlReport.R
8c8a4fc926871f757d13ee77cf8827a4 *R/mergeBreakpoints.R
e29632fa97fb74913ab8aa751579d0a0 *R/methods-AVASet.R
7da4bfa79db1dfddc63707a6657715e4 *R/methods-AnnotatedVariants.R
bab7b378c72387252095f6f84e3d6f84 *R/methods-Breakpoints.R
a886a33cc73375876368f6674e998b7a *R/methods-MapperSet.R
3c00768f8d6d7215c00a8400c1a60dbd *R/methods-Roche454BaseCallerMetrics.R
8db4dd5c61222ad4177e9b7c95b7906b *R/methods-Roche454QualityFilterMetrics.R
9be13791a664cc38e3b32c4b24601b0b *R/methods-SFFContainer.R
a3f898158b2745ba2d61573bc5aea6ee *R/methods-SFFRead.R
f6e4b78d295ebbf069065de915e575d9 *R/plotAmpliconCoverage.R
8f852e6f468cfaa1534c26c3b0a81a39 *R/plotChimericReads.R
45cbd5abf61ea0caff21f52c8608c5d0 *R/plotVariants.R
e5ad25dbde9c3e572cfe984e6419978a *R/plotVariationFrequency.R
77bc46f284a9fba5c122a03348e6911b *R/qualityControl.R
992207e297e806c2a686c12812040f63 *R/qualityReportSFF.R
70cba3bec2c1228b23eb24cbea0cae02 *R/read454BaseCallerMetrics.R
3432099052cada66fef3e0cd97718021 *R/read454QualityFilterMetrics.R
59c8dd7aa295cdce19eda5e47d609251 *R/readSFF.R
928e4d8d15b4a17ada6c6620e2f56fd2 *R/readsOnTarget.R
c6aeb7202b5b7eede60c4f2280a8a975 *R/removeLinker.R
ee8c63c9fae2e7bfb1dfbbb48b550eae *R/sequenceCaptureLinkers.R
d5401ffa078ed3afcab79591053b1faa *R/writeSFF.R
a755cffd1b90cad9076427df9b6e2118 *build/vignette.rds
489b186b7f6972a885de18c594e85909 *data/avaSetExample.RData
b26f9a4853b43a22c73387c7c6cd9eeb *data/avaSetFiltered.RData
c1d944b854d4b800e8a04419c164a882 *data/avaSetFiltered_annot.RData
00f66e479bf2a22e7c67895ac3e35c5e *data/breakpoints.RData
02867656f6aa4d42f525cbabd3bf17c8 *data/captureArray.RData
10ed97379a88bec5258cfc10e7c9e189 *data/mapperSetExample.RData
5a557fe7262c7119f90bcd5cb962011e *data/plotVariantsExample.RData
5827bb0378bb6d9eba4f3b85679b405e *inst/CITATION
ff19d0f3d7b3627da6dd5d0eea0faf78 *inst/NEWS.Rd
808878eae3eb2d7287e3dcc27668a979 *inst/doc/vignette.R
37b80849cdbcd87ad0a376fc2748060a *inst/doc/vignette.Rnw
4ffd22bc8a3dd215447c2ada1c92b389 *inst/doc/vignette.pdf
5c6622b5d96a455a9de472480ff8f168 *inst/extdata/AVASet/Amplicons/ProjectDef/ampliconsProject.txt
f9e763906eef2f97919ac4f794322086 *inst/extdata/AVASet/Amplicons/Results/Align/I116/I36/I116_vs_I36.ampIds.txt
e17e6bd63e2970264d1904079f066427 *inst/extdata/AVASet/Amplicons/Results/Align/I116/I37/I116_vs_I37.ampIds.txt
80b78bdf2a7f8f1139cac00268bf2ff5 *inst/extdata/AVASet/Amplicons/Results/Align/I116/I40/I116_vs_I40.ampIds.txt
1aeb51619e6ca7afc923f64d9f7302e1 *inst/extdata/AVASet/Amplicons/Results/Align/I116/I42/I116_vs_I42.ampIds.txt
1eafca9e2c3a638683c0460d0382a9f8 *inst/extdata/AVASet/Amplicons/Results/Align/I117/I36/I117_vs_I36.ampIds.txt
bf210413caaf7a9419df8e2963975af4 *inst/extdata/AVASet/Amplicons/Results/Align/I117/I37/I117_vs_I37.ampIds.txt
c23bc42f30b688cf4ba5caa2a5ac06f6 *inst/extdata/AVASet/Amplicons/Results/Align/I117/I40/I117_vs_I40.ampIds.txt
6e308d49ab1298c7f1c7eac4b999a61f *inst/extdata/AVASet/Amplicons/Results/Align/I117/I42/I117_vs_I42.ampIds.txt
8688819ae31f6f0081e4d9b505e9122d *inst/extdata/AVASet/Amplicons/Results/Align/I118/I36/I118_vs_I36.ampIds.txt
00da7e73f4fd74e2cf72b09267283b1d *inst/extdata/AVASet/Amplicons/Results/Align/I118/I37/I118_vs_I37.ampIds.txt
ac1a0ef2495e93115911a4eceefb5339 *inst/extdata/AVASet/Amplicons/Results/Align/I118/I40/I118_vs_I40.ampIds.txt
fc082710ac738d02f2d202197e0499ed *inst/extdata/AVASet/Amplicons/Results/Align/I118/I42/I118_vs_I42.ampIds.txt
351eabbfb18cd2cc7eed3a9e3f21f11d *inst/extdata/AVASet/Amplicons/Results/Align/I9644/I36/I9644_vs_I36.ampIds.txt
121d24b7c70335c00b7ed220637e2dc2 *inst/extdata/AVASet/Amplicons/Results/Align/I9644/I37/I9644_vs_I37.ampIds.txt
ef2122319402aad8d30da1b0552dab2c *inst/extdata/AVASet/Amplicons/Results/Align/I9644/I40/I9644_vs_I40.ampIds.txt
77e13c09bf4125adb27b954b77c203c9 *inst/extdata/AVASet/Amplicons/Results/Align/I9644/I42/I9644_vs_I42.ampIds.txt
cdcd883c347cd777080a19d4aa2c65d3 *inst/extdata/AVASet/Amplicons/Results/Align/I9645/I36/I9645_vs_I36.ampIds.txt
2d620873a8819a46d8d545885033cddd *inst/extdata/AVASet/Amplicons/Results/Align/I9645/I37/I9645_vs_I37.ampIds.txt
e8a6d900b91976e7926ca2e50c4cd60b *inst/extdata/AVASet/Amplicons/Results/Align/I9645/I40/I9645_vs_I40.ampIds.txt
633bb52498f8d4b5b90656850bbd1e5d *inst/extdata/AVASet/Amplicons/Results/Align/I9645/I42/I9645_vs_I42.ampIds.txt
f676b6dff2111fd80a0aed08ed179b1a *inst/extdata/AVASet/Amplicons/Results/Align/I9646/I36/I9646_vs_I36.ampIds.txt
d9db7e5f7743f8ea294f3e01c7dbee34 *inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.ampIds.txt
907a02f83e1b3b57cecace640421043d *inst/extdata/AVASet/Amplicons/Results/Align/I9646/I37/I9646_vs_I37.readAlign.txt
20be25a1f9a3aaf7cd44e3a0c62f6690 *inst/extdata/AVASet/Amplicons/Results/Align/I9646/I40/I9646_vs_I40.ampIds.txt
f1421bfaa9dd20742f761ed17bdb4249 *inst/extdata/AVASet/Amplicons/Results/Align/I9646/I42/I9646_vs_I42.ampIds.txt
25732bf3ccfdcd0cd4e3af14e9814102 *inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI36detectedVariants.txt
8ea131293a25d17e6ccc43557279c3e7 *inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI37detectedVariants.txt
2a35c4b7dcfafae61ed38a475fae9855 *inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI40detectedVariants.txt
0da940096b6714b0e05c758e791215e7 *inst/extdata/AVASet/Amplicons/Results/Variants/I116/I116xI42detectedVariants.txt
cffdd0027674433cdfb445377fabcf44 *inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI36detectedVariants.txt
4054216fe8bbe0d9b216ab863f28fcab *inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI37detectedVariants.txt
51ba32c77458a0923ba72f4a1ae37f2d *inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI40detectedVariants.txt
c0c28362fd5ba01a67b7a522ba3d4b16 *inst/extdata/AVASet/Amplicons/Results/Variants/I117/I117xI42detectedVariants.txt
befc098b7639568e29db0bc4e4fd0604 *inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI36detectedVariants.txt
c226e75fa97609530a48c0d3746d9026 *inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI37detectedVariants.txt
e098d40aa1531ec98f227fcbd0d812b4 *inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI40detectedVariants.txt
c7ba99a72c8a05eb3b36180227930ad5 *inst/extdata/AVASet/Amplicons/Results/Variants/I118/I118xI42detectedVariants.txt
9c8d77d0ce629224e01a98b6d416124f *inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI36detectedVariants.txt
b8901eb7b1a09d9762acb8b90b8a53b8 *inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI37detectedVariants.txt
36ed3ebe9c0fd92c90ef7c533fa2ee40 *inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI40detectedVariants.txt
34925a3123b8ed285551baa5f5c3b05d *inst/extdata/AVASet/Amplicons/Results/Variants/I9644/I9644xI42detectedVariants.txt
20ab4c33306e69dac0271644807bdd5e *inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI36detectedVariants.txt
2e04015f25b47c251b5a61ae6d9a33fb *inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI37detectedVariants.txt
a9a627d3ce6061d0f156f6c08981e858 *inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI40detectedVariants.txt
875cbb84c2447d4310cd00bf4ce6ba01 *inst/extdata/AVASet/Amplicons/Results/Variants/I9645/I9645xI42detectedVariants.txt
e4faca18d0584a695042df52fb484c19 *inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI36detectedVariants.txt
3d30342898e09cf1953ab2a0bab611e3 *inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI37detectedVariants.txt
3358f6f755f371172009592d08b23673 *inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI40detectedVariants.txt
356d22e54ecfe7315a7b990230a0263f *inst/extdata/AVASet/Amplicons/Results/Variants/I9646/I9646xI42detectedVariants.txt
0a0f0e703a2c32804aba1910bb7abb55 *inst/extdata/AVASet/Amplicons/Results/Variants/currentVariantDefs.txt
7d15f349a83b32d6c88c8867d7de3e86 *inst/extdata/AVASet_doAmplicon/amp.csv
e6d26ae35b9fb30a4bdf645969335def *inst/extdata/AVASet_doAmplicon/reference.csv
6e533ec95276db04d8d16672a03698a6 *inst/extdata/AVASet_doAmplicon/sample.csv
b8376c2b5e4571c00bdcedc6d2044054 *inst/extdata/AVASet_doAmplicon/variant.csv
457b889cadc492912613fe510b16c882 *inst/extdata/AVASet_doAmplicon/variantHits.csv
a1523ebbbcd6680084ab2af418d53aac *inst/extdata/AVAVarFreqExport/AVAVarFreqExport.xls
d6cb5df93e041924c899cffb4e351365 *inst/extdata/MapperSet/N01/mapping/454HCDiffs.txt
cfd721cf0fbc0361b965f03431033a2e *inst/extdata/MapperSet/N01/mapping/454NewblerMetrics.txt
0123840f6fa81284ee9ba76dc3b816be *inst/extdata/MapperSet/N03/mapping/454HCDiffs.txt
fa1314c513425034298adbd2d14e3863 *inst/extdata/MapperSet/N03/mapping/454NewblerMetrics.txt
6e01c28e047cebcabfe5c3679c765457 *inst/extdata/MapperSet/N04/mapping/454HCDiffs.txt
b2ef968458efdbad265e962b05ff7f4f *inst/extdata/MapperSet/N04/mapping/454NewblerMetrics.txt
e1933ee319d3fb952131e4940e509758 *inst/extdata/SFF/example.sff
57c47448cef42618fd8bada3ec259e0c *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.fna
b1de8bbbf428f9c68971ef61f6a125f4 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.CAT.454Reads.qual
73efee4b14e5652a6ab83269b9b9ab54 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.fna
c43878f368ceeb997c9026c64fbc3f01 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/1.TCA.454Reads.qual
d8b9dfccef6810a6c931a8e84287fee7 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.fna
a456eb560a86f0eb1180a13ba6ca0e38 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.CAT.454Reads.qual
df3ac6f6d393cc83de549f7ddb465dca *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.fna
5be49aabadf4c811b7a1f1f502b5ea20 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/2.TCA.454Reads.qual
8db43e0e4451f5a39155ca7311e432b1 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.csv
b5c28104125e75af2e4d1acdd782bba8 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454BaseCallerMetrics.txt
2598452339aeb58c15441ee7e0514349 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454DataProcessingDir.xml
1307d40d722c219eac816b4e118d9ac8 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.csv
a3cc5f510eeb00cadb78a300c4c5126c *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454QualityFilterMetrics.txt
177d2fe0b330aee89997d3baf1183963 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.csv
715ed7fa09c86baa8e12515139d252a5 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/454RuntimeMetricsAll.txt
4cbd0943f5c0c5e58fa223c3e0d534ae *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/dataRunParams.xml
b10b1b2170b7d951d06ffdcc4d7bc2a9 *inst/extdata/SVDetection/R_2009_07_30/D_2009_07_31/gsRunProcessor.log
aefe78f4da7adb1a866c9ebc911ae92c *inst/extdata/SVDetection/bam/N01.bam
2e8c15949f5d8bfb778d4eaa5ab56c1c *inst/extdata/SVDetection/chip/CaptureArray_hg19.bed
5c757aea2e94fea509af660e4a4b2039 *inst/extdata/qualityReport.Rnw
b103eb1265a62f9f6a7ebf7519891ce7 *inst/javascript/sorttable.js
ad023e4912f7d95d1e30680501156c5f *man/AVASet-class.Rd
a16357142e5258d3f60c1c352e86d018 *man/AVASet.Rd
03e8ab4dac84f9b13ce28b912b075757 *man/AnnotatedVariants-class.Rd
d9e90892c0aeae6bfeeab0ce31b0e4c5 *man/Breakpoints-class.Rd
f93965dd83c38a40fa9128a79a22d820 *man/MapperSet-class.Rd
6f9b70492305b0b9164d8a262e34e669 *man/MapperSet.Rd
562e3b0d9b2d8ff48d6c3fcf5667d686 *man/SFFContainer-class.Rd
645083d3ede33dcc7cf0497896a00de8 *man/SFFRead-class.Rd
d6ef17d717d72ca51ffe0b26c932a012 *man/alignShortReads.Rd
bb7c47b7499b1109b5cdd4ade0795103 *man/annotateVariants.Rd
473241c10c47649c0206bf9611ff7c2e *man/assayDataAmp.Rd
25e88139812426ccc2d71746ebb4c074 *man/ava2vcf.Rd
5bea4be9f7438432c35a5cd9f3baaf8d *man/avaSetExample.Rd
95676bd8a531f02bf53d1ac0c0a7a30b *man/avaSetFiltered.Rd
af46ed5b0a48618f5d2de5fa508d7327 *man/avaSetFiltered_annot.Rd
7a533b0c73af9e89be5460de4629940c *man/baseFrequency.Rd
0e721538d6574eac5ad188890a83e707 *man/baseQualityHist.Rd
e6bdd43db38c36cc12fd7795113b3cd3 *man/baseQualityStats.Rd
387737590f6cbcae450b32c922915477 *man/breakpoints.Rd
40f75b94a450fefc20af149f54e6fcaf *man/calculateTiTv.Rd
aabc3b9b7a175ae1e898f780be85d55c *man/captureArray.Rd
def4edbf13289d10069ed22240cd45ad *man/complexity.dust.Rd
e1f84ebd01748c4d8c4ec76c30fd7545 *man/complexity.entropy.Rd
dcd42c2e2d5dc58c6b60c3cb9b09b225 *man/convertCigar.Rd
7957381ab8e42744370f89071dc807ee *man/coverageOnTarget.Rd
af64849618bc37bd40a8fb68ba297504 *man/demultiplexReads.Rd
0852de761a5828b54a0f729cdd22558c *man/detectBreakpoints.Rd
b8b68ed76eff39a38b417b501cacd496 *man/dinucleotideOddsRatio.Rd
49ffe408768f30c6f885da550634807d *man/fDataAmp.Rd
87f94cb4f236520b64808087d1c0316a *man/featureDataAmp.Rd
74ae08e65b4a68481168170cd20c9a27 *man/filterChimericReads.Rd
7147f64df66b0cd9ee0d218327be4dcf *man/flowgramBarplot.Rd
68d8c28c9183c079e1bcb592efe20481 *man/gcContent.Rd
fa23e1182d6903e3d27673c6a8661303 *man/gcContentHist.Rd
c5d243a62d761197c68add87916181c9 *man/gcPerPosition.Rd
b9b6e8e27ad3d84a13808f7fda679881 *man/genomeSequencerMIDs.Rd
f2bd0649618b5d3ec9ac571819161566 *man/getAlignedReads.Rd
9e333e52a3731d7f8204a134e9861373 *man/getAminoAbbr.Rd
b8924b4e9ed0a8e9af96628c3334e05b *man/getVariantPercentages.Rd
9ea46f4befae2a38b8058ed83b507293 *man/homopolymerHist.Rd
4b5b309006da974769aaf31a24d904fa *man/htmlReport.Rd
a6bb3b34569d15c0e841557c52ad9384 *man/mapperSetExample.Rd
d1e1941594e5bdeb8d2f4ecc0ff92a24 *man/mergeBreakpoints.Rd
29fec08f22c9a7d7db40ecde4c8e3d5a *man/mutationInfo.Rd
b40ab13c919f099cd15ea01242418efa *man/nucleotideCharts.Rd
e9ce6da22d90bfcb8b6f7618860aa786 *man/plotAmpliconCoverage.Rd
56dfa3a82255378b27eb81160a87f6df *man/plotChimericReads.Rd
0a9ce8d5b537fdb558efded835ecc693 *man/plotVariants.Rd
73faf4ba986a4bdcbcc503e66f76abb4 *man/plotVariationFrequency.Rd
8ced8362e3c466c8d37bd1ca2f8e2d94 *man/positionQualityBoxplot.Rd
6eaa9fc9d9cf5194725ace8a03de3088 *man/qualityReportSFF.Rd
06131f1a8da92fc3b40739afa480020f *man/readLengthHist.Rd
b329a0ca2f2e2631d0842b28f4d3f60e *man/readLengthStats.Rd
63f96851459fef96d12eb3f51196f320 *man/readSFF.Rd
9ebce266cbde854efc87a6edbcd99d27 *man/readsOnTarget.Rd
39c900fa8e81fc86afd579d3f871b7f2 *man/referenceSequences.Rd
b3f2a0bc8f127a835a07ea4cafa490d8 *man/regions.Rd
813f980ff8811716b90d7b88578b3f10 *man/removeLinker.Rd
2f02547411f34ad0f0a7e2149e4b0060 *man/sequenceCaptureLinkers.Rd
1e367bc6e8a87cb79694158ba6865f84 *man/sequenceQualityHist.Rd
f7ab30c9396cfa3330a6d5142c872d28 *man/setVariantFilter.Rd
b4e07dc16058786fba281b96feacaa3a *man/sff2fastq.Rd
a69131c5f8932f3a88bee08d1e36d6ea *man/variants.Rd
1b72220d6b4746f894666511ab14694a *man/writeSFF.Rd
ea660916e55f7ca49f057849154c9a97 *src/io_lib/os.h
302a10547acdbef9e9186637d9ee7d9f *src/readSFF.c
879f8f1df167443436552c99676c94ef *src/readSFF.h
79b6177310e0884d288430ec2b735444 *src/writeSFF.c
221f7d422c5c9a540b1834c61f0d1594 *src/writeSFF.h
57b833e3f51c02bc8890dafbf0b34915 *vignettes/plotVariants.pdf
37b80849cdbcd87ad0a376fc2748060a *vignettes/vignette.Rnw
