1. bsseq
  2. Commit 6b3c32334ffcfd3ca9f1413f01d035c12d25fba0
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 21404fe8275c89f6f29231a680703827b0796ff9

Merge pull request #4 from PeteHaitch/master

Updates to read.bismark(), mostly documentation

Commit id: 6ba560784b0e6e6f2e8c40de72b4abf516dc14e3

Update tests and examples to use gzipped data. Ensure strand is kept for cytosineReport files if collapseStrand = FALSE.


Commit id: 41b003506ba63d0c7ec330c2ea0b826e0c1c5e9c

Remove Travis-CI. Not relevant at this juncture.


Commit id: 2fd84392d9f39409b6958f0ce0d77ea5e6476bee

Hardcode RVERSION in .travis.yml


Commit id: 127bc93e92cd065e94dbeac0001949e5c4138d91

Experimental Travis-CI support.


Commit id: a6fecb9692f9b72093d3e0e79cf39e325d63b1e9

Second pass at updating read.bismark() and docs. Updated DESCRIPTION in light of changes and added NEWS.rd entry.


Commit id: 5af9b047653567816174480a6f405e1d02f0a74b

First pass at re-write of read.bismark() and associated docs.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@106909 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 30/07/2015 01:16:09
Showing 13 changed files
.Rbuildignore
History View file @ 6b3c323
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,2 @@
1 
+^.*\.Rproj$
2 
+^\.Rproj\.user$
.gitignore
History View file @ 6b3c323
0 3 
new file mode 100644
... ... 
@@ -0,0 +1,3 @@
1 
+.Rproj.user
2 
+.Rhistory
3 
+.RData
DESCRIPTION
History View file @ 6b3c323
... ... 
@@ -1,17 +1,52 @@
1 1 
 Package: bsseq
2 
-Version: 1.5.4
2 
+Version: 1.5.5
3 3 
 Title: Analyze, manage and store bisulfite sequencing data
4 
-Description: A collection of tools for analyzing and visualizing bisulfite sequencing data.
4 
+Description: A collection of tools for analyzing and visualizing bisulfite
5 
+    sequencing data.
5 6 
 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
6 
-                    email = "kasperdanielhansen@gmail.com"))
7 
-Depends: R (>= 2.15), methods, BiocGenerics, matrixStats, IRanges (>= 2.1.10),
8 
-        GenomicRanges (>= 1.19.6), SummarizedExperiment (>= 0.1.1), parallel,
9 
-        GenomeInfoDb
10 
-Imports: scales, stats, graphics, Biobase, locfit, gtools, data.table, S4Vectors
11 
-Suggests: RUnit, bsseqData, BiocStyle
12 
-Collate: hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R
13 
-        utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R
14 
-        gof_stats.R plotting.R fisher.R permutations.R
7 
+    email = "kasperdanielhansen@gmail.com"),
8 
+    person("Peter", "Hickey", role = "ctb", email = "peter.hickey@gmail.com"))
9 
+Depends:
10 
+    R (>= 2.15),
11 
+    methods,
12 
+    BiocGenerics,
13 
+    IRanges (>= 2.1.10),
14 
+    GenomicRanges (>= 1.19.6),
15 
+    SummarizedExperiment (>= 0.1.1),
16 
+    parallel,
17 
+    GenomeInfoDb
18 
+Imports:
19 
+    scales,
20 
+    stats,
21 
+    graphics,
22 
+    Biobase,
23 
+    locfit,
24 
+    gtools,
25 
+    data.table,
26 
+    S4Vectors,
27 
+    R.utils (>= 2.0.0),
28 
+    matrixStats
29 
+Suggests:
30 
+    RUnit,
31 
+    bsseqData,
32 
+    BiocStyle
33 
+Collate:
34 
+    hasGRanges.R
35 
+    BSseq_class.R
36 
+    BSseqTstat_class.R
37 
+    BSseq_utils.R
38 
+    combine.R
39 
+    utils.R
40 
+    read.bsmooth.R
41 
+    read.bismark.R
42 
+    BSmooth.R
43 
+    BSmooth.tstat.R
44 
+    dmrFinder.R
45 
+    gof_stats.R
46 
+    plotting.R
47 
+    fisher.R
48 
+    permutations.R
49 
+    BSmooth.fstat.R
15 50 
 License: Artistic-2.0
16 51 
 URL: https://github.com/kasperdanielhansen/bsseq
17 52 
 LazyData: yes
NAMESPACE
History View file @ 6b3c323
... ... 
@@ -30,6 +30,7 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo", "seqinf
30 30 
 import(S4Vectors)
31 31 
 importFrom(gtools, "combinations")
32 32 
 importFrom(data.table, "fread", "setnames")
33 
+importFrom(R.utils, "isGzipped", "gunzip")
33 34
34 35 
 ##
35 36 
 ## Exporting
... ... 
@@ -60,7 +61,7 @@ export("BSseq", "getMeth", "getCoverage", "getBSseq", "getStats",
60 61 
        "collapseBSseq", "orderBSseq", "hasBeenSmoothed", "chrSelectBSseq",
61 62 
        "BSmooth", "BSmooth.tstat", "dmrFinder", "fisherTests",
62 63 
        "combineList", "strandCollapse",
63 
-       "plotRegion", "plotManyRegions",
64 
+       "plotRegion", "plotManyRegions",
64 65 
        "read.umtab", "read.umtab2", "read.bsmooth", "read.bismark",
65 66 
        "poissonGoodnessOfFit", "binomialGoodnessOfFit",
66 67 
        "data.frame2GRanges", "BSseqTstat")
R/BSmooth.fstat.R
History View file @ 6b3c323
67 68 
new file mode 100644
... ... 
@@ -0,0 +1,138 @@
1 
+BSmooth.fstat <- function(BSseq, group1, group2, estimate.var = c("same", "paired", "group2"),
2 
+                          local.correct = TRUE, maxGap = NULL, qSd = 0.75, k = 101, mc.cores = 1, verbose = TRUE){
3 
+    smoothSd <- function(Sds, k) {
4 
+        k0 <- floor(k/2)
5 
+        if(all(is.na(Sds))) return(Sds)
6 
+        thresSD <- pmax(Sds, quantile(Sds, qSd, na.rm = TRUE), na.rm = TRUE)
7 
+        addSD <- rep(median(Sds, na.rm = TRUE), k0)
8 
+        sSds <- as.vector(runmean(Rle(c(addSD, thresSD, addSD)), k = k))
9 
+        sSds
10 
+    }
11 
+    compute.correction <- function(idx, qSd = 0.75) {
12 
+        xx <- start(BSseq)[idx]
13 
+        yy <- tstat[idx]
14 
+        suppressWarnings({
15 
+            drange <- diff(range(xx, na.rm = TRUE))
16 
+        })
17 
+        if(drange <= 25000)
18 
+            return(yy)
19 
+        tstat.function <- approxfun(xx, yy)
20 
+        xx.reg <- seq(from = min(xx), to = max(xx), by = 2000)
21 
+        yy.reg <- tstat.function(xx.reg)
22 
+        fit <- locfit(yy.reg ~ lp(xx.reg, h = 25000, deg = 2, nn = 0),
23 
+                      family = "huber", maxk = 50000)
24 
+        correction <- predict(fit, newdata = data.frame(xx.reg = xx))
25 
+        yy - correction
26 
+    }
27 
+
28 
+    estimate.var <- match.arg(estimate.var)
29 
+    stopifnot(is(BSseq, "BSseq"))
30 
+    stopifnot(hasBeenSmoothed(BSseq))
31 
+    if(is.character(group1)) {
32 
+        stopifnot(all(group1 %in% sampleNames(BSseq)))
33 
+        group1 <- match(group1, sampleNames(BSseq))
34 
+    }
35 
+    if(is.numeric(group1)) {
36 
+        stopifnot(min(group1) >= 1 & max(group1) <= ncol(BSseq))
37 
+    } else stop("problems with argument 'group1'")
38 
+    if(is.character(group2)) {
39 
+        stopifnot(all(group2 %in% sampleNames(BSseq)))
40 
+        group2 <- match(group2, sampleNames(BSseq))
41 
+    }
42 
+    if(is.numeric(group2)) {
43 
+        stopifnot(min(group2) >= 1 & max(group2) <= ncol(BSseq))
44 
+    } else stop("problems with argument 'group2'")
45 
+    stopifnot(length(intersect(group1, group2)) == 0)
46 
+    stopifnot(length(group1) > 0)
47 
+    stopifnot(length(group2) > 0)
48 
+    stopifnot(length(group1) + length(group2) >= 3)
49 
+    if(estimate.var == "paired")
50 
+        stopifnot(length(group1) == length(group2))
51 
+
52 
+    if(any(rowSums(getCoverage(BSseq)[, c(group1, group2)]) == 0))
53 
+        warning("Computing f-statistics at locations where there is no data; consider subsetting the 'BSseq' object first")
54 
+
55 
+    if(is.null(maxGap))
56 
+        maxGap <- BSseq@parameters$maxGap
57 
+    if(is.null(maxGap))
58 
+        stop("need to set argument 'maxGap'")
59 
+
60 
+    if(verbose) cat("[BSmooth.fstat] preprocessing ... ")
61 
+    ptime1 <- proc.time()
62 
+    clusterIdx <- makeClusters(BSseq, maxGap = maxGap)
63 
+    ptime2 <- proc.time()
64 
+    stime <- (ptime2 - ptime1)[3]
65 
+    if(verbose) cat(sprintf("done in %.1f sec\n", stime))
66 
+
67 
+    if(verbose) cat("[BSmooth.fstat] computing stats within groups ... ")
68 
+    ptime1 <- proc.time()
69 
+    allPs <- getMeth(BSseq, type = "smooth", what = "perBase",
70 
+                     confint = FALSE)
71 
+    group1.means <- rowMeans(allPs[, group1, drop = FALSE], na.rm = TRUE)
72 
+    group2.means <- rowMeans(allPs[, group2, drop = FALSE], na.rm = TRUE)
73 
+    ptime2 <- proc.time()
74 
+    stime <- (ptime2 - ptime1)[3]
75 
+    if(verbose) cat(sprintf("done in %.1f sec\n", stime))
76 
+
77 
+    if(verbose) cat("[BSmooth.fstat] computing stats across groups ... ")
78 
+    ptime1 <- proc.time()
79 
+    switch(estimate.var,
80 
+           "group2" = {
81 
+               rawSds <- rowSds(allPs[, group2, drop = FALSE], na.rm = TRUE)
82 
+               smoothSds <- do.call(c, mclapply(clusterIdx, function(idx) {
83 
+                   smoothSd(rawSds[idx], k = k)
84 
+               }, mc.cores = mc.cores))
85 
+               scale <- sqrt(1/length(group1) + 1/length(group2))
86 
+               tstat.sd <- smoothSds * scale
87 
+           },
88 
+           "same" = {
89 
+               rawSds <- sqrt( ((length(group1) - 1) * rowVars(allPs[, group1, drop = FALSE]) +
90 
+                                (length(group2) - 1) * rowVars(allPs[, group2, drop = FALSE])) /
91 
+                              (length(group1) + length(group2) - 2))
92 
+               smoothSds <- do.call(c, mclapply(clusterIdx, function(idx) {
93 
+                   smoothSd(rawSds[idx], k = k)
94 
+               }, mc.cores = mc.cores))
95 
+               scale <- sqrt(1/length(group1) + 1/length(group2))
96 
+               tstat.sd <- smoothSds * scale
97 
+           },
98 
+           "paired" = {
99 
+               rawSds <- rowSds(allPs[, group1, drop = FALSE] - allPs[, group2, drop = FALSE])
100 
+               smoothSds <- do.call(c, mclapply(clusterIdx, function(idx) {
101 
+                   smoothSd(rawSds[idx], k = k)
102 
+               }, mc.cores = mc.cores))
103 
+               scale <- sqrt(1/length(group1))
104 
+               tstat.sd <- smoothSds * scale
105 
+           })
106 
+    tstat <- (group1.means - group2.means) / tstat.sd
107 
+    is.na(tstat)[tstat.sd == 0] <- TRUE
108 
+    if(local.correct) {
109 
+        tstat.corrected <- do.call(c, mclapply(clusterIdx,
110 
+                                               compute.correction, qSd = qSd,
111 
+                                               mc.cores = mc.cores))
112 
+    }
113 
+    ptime2 <- proc.time()
114 
+    stime <- (ptime2 - ptime1)[3]
115 
+    if(verbose) cat(sprintf("done in %.1f sec\n", stime))
116 
+
117 
+    if(local.correct) {
118 
+        stats <- cbind(rawSds, tstat.sd, group2.means, group1.means,
119 
+                       tstat, tstat.corrected)
120 
+        colnames(stats) <- c("rawSds", "tstat.sd",
121 
+                             "group2.means", "group1.means", "tstat",
122 
+                             "tstat.corrected")
123 
+
124 
+    } else {
125 
+        stats <- cbind(rawSds, tstat.sd, group2.means, group1.means,
126 
+                       tstat)
127 
+        colnames(stats) <- c("rawSds", "tstat.sd",
128 
+                             "group2.means", "group1.means", "tstat")
129 
+    }
130 
+
131 
+    parameters <- c(BSseq@parameters,
132 
+                    list(tstatText = sprintf("BSmooth.fstat (local.correct = %s, maxGap = %d)",
133 
+                         local.correct, maxGap),
134 
+                         group1 = group1, group2 = group2, k = k, qSd = qSd,
135 
+                         local.correct = local.correct, maxGap = maxGap))
136 
+    out <- BSseqTstat(gr = granges(BSseq), stats = stats, parameters = parameters)
137 
+    out
138 
+}
R/read.bismark.R
History View file @ 6b3c323
... ... 
@@ -1,98 +1,125 @@
1 
-read.bismark <- function(files, sampleNames, rmZeroCov = FALSE, strandCollapse = TRUE,
2 
-                         fileType = c("cytosineReport", "oldBedGraph"), verbose = TRUE){
1 
+read.bismark <- function(files,
2 
+                         sampleNames,
3 
+                         rmZeroCov = FALSE,
4 
+                         strandCollapse = TRUE,
5 
+                         fileType = c("cov", "oldBedGraph", "cytosineReport"),
6 
+                         verbose = TRUE) {
3 7 
     ## Argument checking
4 
-    if (anyDuplicated(files)){
8 
+    if (anyDuplicated(files)) {
5 9 
         stop("duplicate entries in 'files'")
6 10 
     }
7 
-    if (length(sampleNames) != length(files) | anyDuplicated(sampleNames)){
11 
+    if (length(sampleNames) != length(files) || anyDuplicated(sampleNames)) {
8 12 
         stop("argument 'sampleNames' has to have the same length as argument 'files', without duplicate entries")
9 13 
     }
10 14 
     fileType <- match.arg(fileType)
15 
+    if (verbose) {
16 
+        message(paste0("Assuming file type is", fileType))
17 
+    }
11 18 
     ## Process each file
12 19 
     idxes <- seq_along(files)
13 20 
     names(idxes) <- sampleNames
14 
-    allOut <- lapply(idxes, function(ii){
21 
+    allOut <- lapply(idxes, function(ii) {
15 22 
         if (verbose) {
16 23 
             cat(sprintf("[read.bismark] Reading file '%s' ... ", files[ii]))
17 24 
         }
18 25 
         ptime1 <- proc.time()
19 
-        if(fileType == "oldBedGraph") {
20 
-            raw <- read.bismarkFileRaw(thisfile = files[ii])
21 
-        }
22 
-        if(fileType == "cytosineReport") {
23 
-            raw <- read.bismarkCytosineRaw(thisfile = files[ii], keepContext = FALSE)
26 
+        if (fileType == "cov" || fileType == "oldBedGraph") {
27 
+            out <- read.bismarkCovRaw(thisfile = files[ii],
28 
+                                      thisSampleName = sampleNames[ii],
29 
+                                      rmZeroCov = rmZeroCov)
30 
+        } else if (fileType == "cytosineReport") {
31 
+            out <- read.bismarkCytosineReportRaw(thisfile = files[ii],
32 
+                                                 thisSampleName = sampleNames[ii],
33 
+                                                 rmZeroCov = rmZeroCov,
34 
+                                                 keepContext = FALSE)
24 35 
         }
25 
-        M <- matrix(mcols(raw)[, "mCount"], ncol = 1)
26 
-        Cov <- M + mcols(raw)[, "uCount"]
27 
-        mcols(raw) <- NULL
28 
-        out <- BSseq(gr = raw, M = M, Cov = Cov,
29 
-                     sampleNames = sampleNames[ii], rmZeroCov = rmZeroCov)
30 
-        if(strandCollapse && !all(runValue(strand(out)) == "*"))
36 
+        if (strandCollapse && !all(runValue(strand(out)) == "*")) {
31 37 
             out <- strandCollapse(out)
38 
+        }
32 39 
         ptime2 <- proc.time()
33 40 
         stime <- (ptime2 - ptime1)[3]
34 41 
         if (verbose) {
35 
-            cat(sprintf("done in %.1f secs\n", stime))
42 
+            cat(sprintf("done in %.1f secs\n", stime))
36 43 
         }
37 
-        out
44 
+        out
38 45 
     })
46 
+
39 47 
     if (verbose) {
40 48 
         cat(sprintf("[read.bismark] Joining samples ... "))
41 49 
     }
42 50 
     ptime1 <- proc.time()
43 51 
     allOut <- combineList(allOut)
44 52 
     ptime2 <- proc.time()
45 
-    stime <- (ptime2 - ptime1)[3]
53 
+    stime <- (ptime2 - ptime1)[3L]
46 54 
     if (verbose) {
47 55 
         cat(sprintf("done in %.1f secs\n", stime))
48 56 
     }
49 57 
     allOut
50 58 
 }
51 59
52 
-read.bismarkFileRaw <- function(thisfile, verbose = TRUE){
53 
-    ## Set up the 'what' argument for scan()
54 
-    columnHeaders <- c("chr", "start", "end", "mPerc", "mCount", "uCount")
55 
-    what0 <- replicate(length(columnHeaders), character(0))
56 
-    names(what0) <- columnHeaders
57 
-    int <- which(columnHeaders %in% c("start", "end", "mCount", "uCount"))
58 
-    what0[int] <- replicate(length(int), integer(0))
59 
-    null <- which(columnHeaders %in% "mPerc")
60 
-    what0[null] <- replicate(length(null), NULL)
60 
+read.bismarkCovRaw <- function(thisfile,
61 
+                               thisSampleName,
62 
+                               rmZeroCov) {
63 
+
64 
+    ## data.table::fread() can't read directly from a gzipped file so, if
65 
+    ## necessary, gunzip the file to a temporary location.
66 
+    if (isGzipped(thisfile)) {
67 
+        thisfile <- gunzip(thisfile,
68 
+                           temporary = TRUE,
69 
+                           overwrite = TRUE,
70 
+                           remove = FALSE)
71 
+    }
72 
+
61 73 
     ## Read in the file
62 
-    if (grepl("\\.gz$", thisfile))
63 
-        con <- gzfile(thisfile)
64 
-    else
65 
-        con <- file(thisfile, open = "r")
66 
-    out <- scan(file = con, what = what0, sep = "\t", quote = "", na.strings = "NA", quiet = TRUE)
67 
-    close(con)
74 
+    out <- fread(thisfile)
75 
+    if (ncol(out) != 6L) {
76 
+        stop("unknown file format")
77 
+    }
78 
+
68 79 
     ## Create GRanges instance from 'out'
69 
-    gr <- GRanges(seqnames = out[["chr"]], ranges = IRanges(start = out[["start"]], width = 1))
70 
-    out[["chr"]] <- out[["start"]] <- out[["end"]] <- NULL
71 
-    out <- out[!sapply(out, is.null)]
72 
-    df <- DataFrame(out)
73 
-    mcols(gr) <- df
74 
-    gr
80 
+    gr <- GRanges(seqnames = out[[1L]],
81 
+                  ranges = IRanges(start = out[[2L]], width = 1L))
82 
+
83 
+    ## Create BSseq instance from 'out'
84 
+    BSseq(gr = gr,
85 
+          M = as.matrix(out[[5L]]),
86 
+          Cov = as.matrix(out[[5L]] + out[[6L]]),
87 
+          sampleNames = thisSampleName,
88 
+          rmZeroCov = rmZeroCov)
75 89 
 }
76 90
77 
-read.bismarkCytosineRaw <- function(thisfile, keepContext = FALSE) {
91 
+read.bismarkCytosineReportRaw <- function(thisfile,
92 
+                                          thisSampleName,
93 
+                                          rmZeroCov,
94 
+                                          keepContext = FALSE) {
95 
+
96 
+    ## NOTE: keepContext not yet implemented
97 
+    if (keepContext) {
98 
+        stop("'keepContext' argument not yet implemented")
99 
+    }
100 
+
101 
+    ## data.table::fread() can't read directly from a gzipped file so, if
102 
+    ## necessary, gunzip the file to a temporary location.
103 
+    if (isGzipped(thisfile)) {
104 
+        thisfile <- gunzip(thisfile,
105 
+                           temporary = TRUE,
106 
+                           overwrite = TRUE,
107 
+                           remove = FALSE)
108 
+    }
109 
+
110 
+    ## Read in the file
78 111 
     out <- fread(thisfile)
79 
-    if(length(out) != 6 && length(out) != 7)
112 
+    if (ncol(out) != 7L) {
80 113 
         stop("unknown file format")
81 
-    if(length(out) == 6) {
82 
-        setnames(out, c("chr", "start", "end", "methPerc", "mCount", "uCount"))
83 
-        gr <- GRanges(seqnames = out[["chr"]],
84 
-                      ranges = IRanges(start = out[["start"]], width = 1),
85 
-                      mCount = out[["mCount"]], uCount = out[["uCount"]])
86 
-    }
87 
-    if(length(out) == 7) {
88 
-        setnames(out, c("chr", "start", "strand", "mCount", "uCount", "type", "context"))
89 
-        gr <- GRanges(seqnames = out[["chr"]], strand = out[["strand"]],
90 
-                      ranges = IRanges(start = out[["start"]], width = 1),
91 
-                      mCount = out[["mCount"]], uCount = out[["uCount"]])
92 
-        if(keepContext) {
93 
-            gr$type <- out[["type"]]
94 
-            gr$context <- out[["context"]]
95 
-        }
96 114 
     }
97 
-    gr
115 
+
116 
+    ## Create GRanges instance from 'out'
117 
+    gr <- GRanges(seqnames = out[[1]],
118 
+                  ranges = IRanges(start = out[[2]], width = 1),
119 
+                  strand = out[[3]])
120 
+
121 
+    ## Create BSseq instance from 'out'
122 
+    BSseq(gr = gr,
123 
+          M = as.matrix(out[[4L]]),
124 
+          Cov = as.matrix(out[[4L]] + out[[5L]]))
98 125 
 }
bsseq.Rproj
History View file @ 6b3c323
99 126 
new file mode 100644
... ... 
@@ -0,0 +1,20 @@
1 
+Version: 1.0
2 
+
3 
+RestoreWorkspace: Default
4 
+SaveWorkspace: Default
5 
+AlwaysSaveHistory: Default
6 
+
7 
+EnableCodeIndexing: Yes
8 
+UseSpacesForTab: Yes
9 
+NumSpacesForTab: 4
10 
+Encoding: UTF-8
11 
+
12 
+RnwWeave: knitr
13 
+LaTeX: pdfLaTeX
14 
+
15 
+AutoAppendNewline: Yes
16 
+StripTrailingWhitespace: Yes
17 
+
18 
+BuildType: Package
19 
+PackageUseDevtools: Yes
20 
+PackageInstallArgs: --no-multiarch --with-keep.source
inst/NEWS.Rd
History View file @ 6b3c323
... ... 
@@ -6,8 +6,11 @@
6 6 
   \itemize{
7 7 
     \item new function strandCollapse for collapsing forward and reverse
8 8 
     strand data to be unstranded.
9 
-    \item Updated read.bismark to support the cytosine report files;
10 
-    both formats are support.
9 
+    \item Updated read.bismark() to support the cytosine report files;
10 
+    both formats are supported. Other minor updates (mostly internal) to
11 
+    read.bismark(). Greatly improved documentation of this function, paying
12 
+    particular attention to differences in file formats between versions of
13 
+    Bismark.
11 14 
   }
12 15 
 }
13 16
... ... 
@@ -103,7 +106,7 @@
103 106 
     combineList for testing.
104 107 
     \item Bug fix to read.bsmooth; it now works correctly for the
105 108 
     default settings (= returning a single object of class BSseq and not a
106 
-    list).
109 
+    list).
107 110 
     \item Getting ready for initial release on Bioconductor.
108 111 
     \item Updated the citations in the vignette(s) and the CITATION file.
109 112 
   }
inst/extdata/CpG_context_test_data.fastq_bismark.bedGraph
History View file @ 6b3c323
110 113 
deleted file mode 100644
... ... 
@@ -1,2013 +0,0 @@
1 
-chr1	910855	910855	100	1	0
2 
-chr1	910867	910867	100	1	0
3 
-chr1	910869	910869	100	1	0
4 
-chr1	2155925	2155925	100	1	0
5 
-chr1	2155927	2155927	100	1	0
6 
-chr1	2155952	2155952	100	1	0
7 
-chr1	2155958	2155958	100	1	0
8 
-chr1	2244658	2244658	0	0	1
9 
-chr1	9373960	9373960	100	1	0
10 
-chr1	9373972	9373972	100	1	0
11 
-chr1	9374005	9374005	100	1	0
12 
-chr1	14834883	14834883	100	1	0
13 
-chr1	14834894	14834894	100	1	0
14 
-chr1	14834913	14834913	100	1	0
15 
-chr1	14834924	14834924	100	1	0
16 
-chr1	14834931	14834931	100	1	0
17 
-chr1	17902566	17902566	100	1	0
18 
-chr1	17902573	17902573	100	1	0
19 
-chr1	19367741	19367741	0	0	1
20 
-chr1	19591662	19591662	100	1	0
21 
-chr1	20087539	20087539	100	1	0
22 
-chr1	21124142	21124142	100	1	0
23 
-chr1	21124172	21124172	100	1	0
24 
-chr1	21865336	21865336	100	1	0
25 
-chr1	24778917	24778917	100	1	0
26 
-chr1	25345009	25345009	0	0	1
27 
-chr1	26092681	26092681	0	0	1
28 
-chr1	29272768	29272768	100	1	0
29 
-chr1	29272776	29272776	100	1	0
30 
-chr1	30606039	30606039	0	0	1
31 
-chr1	31265293	31265293	100	1	0
32 
-chr1	31265325	31265325	100	1	0
33 
-chr1	32135830	32135830	100	1	0
34 
-chr1	33070548	33070548	100	1	0
35 
-chr1	33070579	33070579	100	1	0
36 
-chr1	33579808	33579808	100	1	0
37 
-chr1	33579812	33579812	0	0	1
38 
-chr1	33579827	33579827	100	1	0
39 
-chr1	36897877	36897877	100	1	0
40 
-chr1	39735623	39735623	100	1	0
41 
-chr1	45178880	45178880	100	1	0
42 
-chr1	45178895	45178895	100	1	0
43 
-chr1	47949737	47949737	100	1	0
44 
-chr1	50957421	50957421	100	1	0
45 
-chr1	51693113	51693113	100	1	0
46 
-chr1	51693117	51693117	100	1	0
47 
-chr1	57798690	57798690	0	0	1
48 
-chr1	61157310	61157310	0	0	1
49 
-chr1	64010066	64010066	100	1	0
50 
-chr1	65450469	65450469	100	1	0
51 
-chr1	65450487	65450487	0	0	1
52 
-chr1	65987569	65987569	100	1	0
53 
-chr1	65987611	65987611	100	1	0
54 
-chr1	68729100	68729100	100	1	0
55 
-chr1	71489973	71489973	100	1	0
56 
-chr1	71489977	71489977	100	1	0
57 
-chr1	73497556	73497556	0	0	1
58 
-chr1	73956692	73956692	0	0	1
59 
-chr1	73956727	73956727	0	0	1
60 
-chr1	85725838	85725838	0	0	1
61 
-chr1	89316500	89316500	100	1	0
62 
-chr1	89891247	89891247	100	1	0
63 
-chr1	89891262	89891262	100	1	0
64 
-chr1	89891271	89891271	100	1	0
65 
-chr1	89891285	89891285	100	1	0
66 
-chr1	93820273	93820273	100	1	0
67 
-chr1	94141914	94141914	100	1	0
68 
-chr1	96838711	96838711	100	1	0
69 
-chr1	98058817	98058817	100	1	0
70 
-chr1	99698820	99698820	100	1	0
71 
-chr1	101054920	101054920	100	1	0
72 
-chr1	105700060	105700060	0	0	1
73 
-chr1	107677718	107677718	100	1	0
74 
-chr1	107677726	107677726	100	1	0
75 
-chr1	108408057	108408057	100	1	0
76 
-chr1	109961437	109961437	100	1	0
77 
-chr1	110547937	110547937	100	1	0
78 
-chr1	111372071	111372071	100	1	0
79 
-chr1	117693870	117693870	100	1	0
80 
-chr1	120016132	120016132	100	1	0
81 
-chr1	120274693	120274693	100	1	0
82 
-chr1	121484800	121484800	0	0	1
83 
-chr1	121485140	121485140	0	0	1
84 
-chr1	121485290	121485290	0	0	1
85 
-chr1	146885280	146885280	100	1	0
86 
-chr1	149068394	149068394	100	1	0
87 
-chr1	152025762	152025762	0	0	1
88 
-chr1	153235818	153235818	100	1	0
89 
-chr1	153235840	153235840	100	1	0
90 
-chr1	156714383	156714383	100	1	0
91 
-chr1	156935169	156935169	100	1	0
92 
-chr1	157636689	157636689	0	0	1
93 
-chr1	158627600	158627600	0	0	1
94 
-chr1	158627603	158627603	100	1	0
95 
-chr1	165389626	165389626	100	1	0
96 
-chr1	165777638	165777638	100	1	0
97 
-chr1	165777648	165777648	100	1	0
98 
-chr1	165777650	165777650	100	1	0
99 
-chr1	165777654	165777654	100	1	0
100 
-chr1	166097119	166097119	0	0	1
101 
-chr1	169453550	169453550	100	1	0
102 
-chr1	170661536	170661536	100	1	0
103 
-chr1	173030868	173030868	100	1	0
104 
-chr1	173259947	173259947	100	1	0
105 
-chr1	175221718	175221718	0	0	1
106 
-chr1	180530889	180530889	100	1	0
107 
-chr1	180530896	180530896	100	1	0
108 
-chr1	181452242	181452242	0	0	1
109 
-chr1	181452276	181452276	0	0	1
110 
-chr1	181452278	181452278	0	0	1
111 
-chr1	184780698	184780698	100	1	0
112 
-chr1	184780700	184780700	100	1	0
113 
-chr1	185017023	185017023	100	1	0
114 
-chr1	185196893	185196893	100	1	0
115 
-chr1	185196906	185196906	100	1	0
116 
-chr1	185710761	185710761	100	1	0
117 
-chr1	187850494	187850494	0	0	1
118 
-chr1	190397573	190397573	100	1	0
119 
-chr1	192022368	192022368	100	1	0
120 
-chr1	202620443	202620443	0	0	1
121 
-chr1	202620478	202620478	0	0	1
122 
-chr1	204094430	204094430	100	1	0
123 
-chr1	207580583	207580583	0	0	1
124 
-chr1	210423288	210423288	0	0	1
125 
-chr1	211207514	211207514	100	1	0
126 
-chr1	211656955	211656955	0	0	1
127 
-chr1	212559488	212559488	0	0	1
128 
-chr1	213276858	213276858	100	1	0
129 
-chr1	214157482	214157482	0	0	1
130 
-chr1	218716809	218716809	100	1	0
131 
-chr1	218716840	218716840	100	1	0
132 
-chr1	219098216	219098216	100	1	0
133 
-chr1	222160425	222160425	100	1	0
134 
-chr1	224853105	224853105	0	0	1
135 
-chr1	224853131	224853131	100	1	0
136 
-chr1	225911616	225911616	100	1	0
137 
-chr1	227273698	227273698	100	1	0
138 
-chr1	228490956	228490956	100	1	0
139 
-chr1	230250675	230250675	0	0	1
140 
-chr1	230363799	230363799	0	0	1
141 
-chr1	230500625	230500625	100	1	0
142 
-chr1	233164872	233164872	100	1	0
143 
-chr1	234700743	234700743	0	0	1
144 
-chr1	234844236	234844236	100	1	0
145 
-chr1	236956932	236956932	100	1	0
146 
-chr1	236956939	236956939	100	1	0
147 
-chr1	236956967	236956967	100	1	0
148 
-chr1	239941034	239941034	100	1	0
149 
-chr1	240845242	240845242	100	1	0
150 
-chr1	240867524	240867524	100	1	0
151 
-chr1	241170319	241170319	0	0	1
152 
-chr1	245746844	245746844	100	1	0
153 
-chr1	245746872	245746872	0	0	1
154 
-chr10	4141341	4141341	100	1	0
155 
-chr10	4612106	4612106	100	1	0
156 
-chr10	6240790	6240790	100	1	0
157 
-chr10	6764445	6764445	0	0	1
158 
-chr10	8370320	8370320	0	0	1
159 
-chr10	13752701	13752701	100	1	0
160 
-chr10	14851718	14851718	0	0	1
161 
-chr10	14851741	14851741	100	1	0
162 
-chr10	15544140	15544140	100	1	0
163 
-chr10	16706274	16706274	100	1	0
164 
-chr10	16706309	16706309	100	1	0
165 
-chr10	16783740	16783740	100	1	0
166 
-chr10	20647278	20647278	100	1	0
167 
-chr10	22208118	22208118	0	0	1
168 
-chr10	22405338	22405338	0	0	1
169 
-chr10	25895949	25895949	100	1	0
170 
-chr10	26821219	26821219	0	0	1
171 
-chr10	26932274	26932274	0	0	1
172 
-chr10	28004690	28004690	100	1	0
173 
-chr10	28004723	28004723	100	1	0
174 
-chr10	29277611	29277611	100	1	0
175 
-chr10	32344149	32344149	0	0	1
176 
-chr10	33652698	33652698	100	1	0
177 
-chr10	33909881	33909881	100	1	0
178 
-chr10	34111056	34111056	100	1	0
179 
-chr10	35753685	35753685	0	0	1
180 
-chr10	37175841	37175841	0	0	1
181 
-chr10	38516400	38516400	0	0	1
182 
-chr10	38603878	38603878	0	0	1
183 
-chr10	39106324	39106324	100	1	0
184 
-chr10	39106354	39106354	0	0	1
185 
-chr10	42380273	42380273	0	0	1
186 
-chr10	42380648	42380648	0	0	1
187 
-chr10	42392728	42392728	100	2	0
188 
-chr10	42392741	42392741	100	2	0
189 
-chr10	42392751	42392751	100	1	0
190 
-chr10	42396001	42396001	100	1	0
191 
-chr10	42396014	42396014	100	1	0
192 
-chr10	42396024	42396024	100	1	0
193 
-chr10	42396037	42396037	100	1	0
194 
-chr10	42396982	42396982	100	1	0
195 
-chr10	42396992	42396992	100	1	0
196 
-chr10	42396997	42396997	0	0	1
197 
-chr10	42397005	42397005	100	1	0
198 
-chr10	42600027	42600027	100	1	0
199 
-chr10	42600047	42600047	100	2	0
200 
-chr10	42600069	42600069	100	2	0
201 
-chr10	47064847	47064847	100	1	0
202 
-chr10	48033086	48033086	0	0	1
203 
-chr10	52750904	52750904	0	0	1
204 
-chr10	52750930	52750930	0	0	1
205 
-chr10	54808911	54808911	100	1	0
206 
-chr10	59135477	59135477	100	1	0
207 
-chr10	60205318	60205318	100	1	0
208 
-chr10	64613501	64613501	0	0	1
209 
-chr10	65684759	65684759	100	1	0
210 
-chr10	72043308	72043308	0	0	1
211 
-chr10	73022729	73022729	0	0	1
212 
-chr10	73668963	73668963	100	1	0
213 
-chr10	75936200	75936200	0	0	1
214 
-chr10	75936218	75936218	0	0	1
215 
-chr10	83211055	83211055	100	1	0
216 
-chr10	90818899	90818899	100	1	0
217 
-chr10	93711102	93711102	100	1	0
218 
-chr10	97017240	97017240	100	1	0
219 
-chr10	97025815	97025815	100	1	0
220 
-chr10	99192404	99192404	100	1	0
221 
-chr10	99192444	99192444	100	1	0
222 
-chr10	105004311	105004311	0	0	1
223 
-chr10	106893217	106893217	100	1	0
224 
-chr10	107109685	107109685	0	0	1
225 
-chr10	107109691	107109691	0	0	1
226 
-chr10	108162607	108162607	100	1	0
227 
-chr10	108361036	108361036	100	1	0
228 
-chr10	109290805	109290805	0	0	1
229 
-chr10	110170844	110170844	100	1	0
230 
-chr10	111939341	111939341	100	1	0
231 
-chr10	111939370	111939370	100	1	0
232 
-chr10	111992065	111992065	100	1	0
233 
-chr10	111992067	111992067	100	1	0
234 
-chr10	115578146	115578146	100	1	0
235 
-chr10	115946788	115946788	0	0	1
236 
-chr10	116475250	116475250	0	0	1
237 
-chr10	116883055	116883055	0	0	1
238 
-chr10	117105927	117105927	100	1	0
239 
-chr10	117936764	117936764	0	0	1
240 
-chr10	117936776	117936776	0	0	1
241 
-chr10	118926838	118926838	0	0	1
242 
-chr10	121354583	121354583	100	1	0
243 
-chr10	121354588	121354588	100	1	0
244 
-chr10	123376744	123376744	100	1	0
245 
-chr10	123833783	123833783	100	1	0
246 
-chr10	127150630	127150630	0	0	1
247 
-chr10	127150637	127150637	0	0	1
248 
-chr10	129730484	129730484	100	1	0
249 
-chr10	130227742	130227742	0	0	1
250 
-chr10	131367500	131367500	0	0	1
251 
-chr10	131367506	131367506	100	1	0
252 
-chr10	131367509	131367509	100	1	0
253 
-chr10	133809212	133809212	100	1	0
254 
-chr10	133809242	133809242	100	1	0
255 
-chr10	135221387	135221387	100	1	0
256 
-chr11	4539502	4539502	100	1	0
257 
-chr11	5332514	5332514	0	0	1
258 
-chr11	6712589	6712589	100	1	0
259 
-chr11	7986140	7986140	100	1	0
260 
-chr11	8392519	8392519	100	1	0
261 
-chr11	8392539	8392539	100	1	0
262 
-chr11	10107756	10107756	0	0	1
263 
-chr11	11564092	11564092	0	0	1
264 
-chr11	16628884	16628884	0	0	1
265 
-chr11	16628896	16628896	0	0	1
266 
-chr11	16628914	16628914	100	1	0
267 
-chr11	16628916	16628916	0	0	1
268 
-chr11	16628918	16628918	0	0	1
269 
-chr11	17670884	17670884	0	0	1
270 
-chr11	19166383	19166383	100	1	0
271 
-chr11	20500804	20500804	100	1	0
272 
-chr11	20500821	20500821	100	1	0
273 
-chr11	21871951	21871951	100	1	0
274 
-chr11	21871985	21871985	0	0	1
275 
-chr11	22626020	22626020	100	1	0
276 
-chr11	23908670	23908670	100	1	0
277 
-chr11	30744332	30744332	0	0	1
278 
-chr11	31980101	31980101	0	0	1
279 
-chr11	34952869	34952869	100	1	0
280 
-chr11	35165854	35165854	100	1	0
281 
-chr11	37743813	37743813	100	1	0
282 
-chr11	41808530	41808530	0	0	1
283 
-chr11	44365953	44365953	0	0	1
284 
-chr11	44822124	44822124	100	1	0
285 
-chr11	44822142	44822142	100	1	0
286 
-chr11	46640740	46640740	100	1	0
287 
-chr11	46861409	46861409	100	1	0
288 
-chr11	47752078	47752078	100	1	0
289 
-chr11	48146157	48146157	100	1	0
290 
-chr11	49846188	49846188	100	1	0
291 
-chr11	49846212	49846212	100	1	0
292 
-chr11	54795357	54795357	0	0	1
293 
-chr11	54795365	54795365	100	1	0
294 
-chr11	54795386	54795386	100	1	0
295 
-chr11	59032467	59032467	100	1	0
296 
-chr11	61430639	61430639	0	0	1
297 
-chr11	61430643	61430643	100	1	0
298 
-chr11	64284142	64284142	100	1	0
299 
-chr11	66780216	66780216	0	0	1
300 
-chr11	68492599	68492599	100	1	0
301 
-chr11	69867751	69867751	100	1	0
302 
-chr11	69867766	69867766	0	0	1
303 
-chr11	69867770	69867770	0	0	1
304 
-chr11	69867787	69867787	100	1	0
305 
-chr11	69932960	69932960	100	1	0
306 
-chr11	73061855	73061855	100	1	0
307 
-chr11	73061896	73061896	100	1	0
308 
-chr11	77048068	77048068	100	1	0
309 
-chr11	77736288	77736288	100	1	0
310 
-chr11	78674351	78674351	100	1	0
311 
-chr11	79239919	79239919	100	1	0
312 
-chr11	79497080	79497080	0	0	1
313 
-chr11	84194467	84194467	0	0	1
314 
-chr11	85497628	85497628	100	1	0
315 
-chr11	88785903	88785903	0	0	1
316 
-chr11	89866428	89866428	100	1	0
317 
-chr11	94370539	94370539	100	1	0
318 
-chr11	101079905	101079905	100	1	0
319 
-chr11	105481777	105481777	0	0	1
320 
-chr11	105481794	105481794	0	0	1
321 
-chr11	105481801	105481801	0	0	1
322 
-chr11	106336172	106336172	100	1	0
323 
-chr11	108895739	108895739	100	1	0
324 
-chr11	109111057	109111057	100	1	0
325 
-chr11	109122704	109122704	100	1	0
326 
-chr11	112604608	112604608	0	0	1
327 
-chr11	115240600	115240600	100	1	0
328 
-chr11	115579741	115579741	0	0	1
329 
-chr11	119891041	119891041	0	0	1
330 
-chr11	120407551	120407551	100	1	0
331 
-chr11	120407562	120407562	100	1	0
332 
-chr11	120453184	120453184	0	0	1
333 
-chr11	124860179	124860179	0	0	1
334 
-chr11	125408135	125408135	100	1	0
335 
-chr11	126497852	126497852	100	1	0
336 
-chr11	133594211	133594211	100	1	0
337 
-chr11	133594237	133594237	0	0	1
338 
-chr12	672871	672871	100	1	0
339 
-chr12	3320514	3320514	100	1	0
340 
-chr12	4606631	4606631	100	1	0
341 
-chr12	4955101	4955101	0	0	1
342 
-chr12	5113508	5113508	100	1	0
343 
-chr12	5113524	5113524	100	1	0
344 
-chr12	8041033	8041033	100	1	0
345 
-chr12	9946217	9946217	100	1	0
346 
-chr12	12029943	12029943	100	1	0
347 
-chr12	12086177	12086177	100	1	0
348 
-chr12	15269090	15269090	0	0	1
349 
-chr12	19568059	19568059	100	1	0
350 
-chr12	19568064	19568064	100	1	0
351 
-chr12	20836775	20836775	100	1	0
352 
-chr12	20836794	20836794	100	1	0
353 
-chr12	22791865	22791865	100	1	0
354 
-chr12	26662529	26662529	0	0	1
355 
-chr12	28193066	28193066	100	1	0
356 
-chr12	28323281	28323281	100	1	0
357 
-chr12	32162575	32162575	100	1	0
358 
-chr12	32162585	32162585	100	1	0
359 
-chr12	32162591	32162591	100	1	0
360 
-chr12	32162617	32162617	100	1	0
361 
-chr12	34288315	34288315	100	1	0
362 
-chr12	34530844	34530844	0	0	1
363 
-chr12	34530874	34530874	0	0	1
364 
-chr12	34700377	34700377	100	1	0
365 
-chr12	34700385	34700385	0	0	1
366 
-chr12	39463421	39463421	0	0	1
367 
-chr12	46642079	46642079	100	1	0
368 
-chr12	52642929	52642929	0	0	1
369 
-chr12	53475444	53475444	100	1	0
370 
-chr12	60592035	60592035	100	1	0
371 
-chr12	60592045	60592045	100	1	0
372 
-chr12	64083609	64083609	100	1	0
373 
-chr12	66054031	66054031	100	1	0
374 
-chr12	67710666	67710666	100	1	0
375 
-chr12	69789923	69789923	0	0	1
376 
-chr12	72169610	72169610	0	0	1
377 
-chr12	74078835	74078835	0	0	1
378 
-chr12	74199104	74199104	0	0	1
379 
-chr12	75182084	75182084	100	1	0
380 
-chr12	78284617	78284617	100	1	0
381 
-chr12	83618051	83618051	100	1	0
382 
-chr12	85812883	85812883	0	0	1
383 
-chr12	85812897	85812897	100	1	0
384 
-chr12	86994889	86994889	100	1	0
385 
-chr12	86994897	86994897	100	1	0
386 
-chr12	88640910	88640910	100	1	0
387 
-chr12	89730151	89730151	100	1	0
388 
-chr12	92073686	92073686	100	1	0
389 
-chr12	93760418	93760418	0	0	1
390 
-chr12	93760451	93760451	100	1	0
391 
-chr12	95798581	95798581	100	1	0
392 
-chr12	98064601	98064601	0	0	1
393 
-chr12	98544445	98544445	0	0	1
394 
-chr12	98796841	98796841	0	0	1
395 
-chr12	99188328	99188328	100	1	0
396 
-chr12	99289824	99289824	0	0	1
397 
-chr12	100028578	100028578	100	1	0
398 
-chr12	101420409	101420409	100	1	0
399 
-chr12	105655621	105655621	100	1	0
400 
-chr12	108198595	108198595	0	0	1
401 
-chr12	109834024	109834024	0	0	1
402 
-chr12	111270823	111270823	0	0	1
403 
-chr12	114242486	114242486	0	0	1
404 
-chr12	114242517	114242517	100	1	0
405 
-chr12	114242522	114242522	100	1	0
406 
-chr12	116661364	116661364	100	1	0
407 
-chr12	116661378	116661378	100	1	0
408 
-chr12	117676990	117676990	0	0	1
409 
-chr12	117818791	117818791	0	0	1
410 
-chr12	121807408	121807408	100	1	0
411 
-chr12	121807420	121807420	100	1	0
412 
-chr12	121807425	121807425	100	1	0
413 
-chr12	123690923	123690923	100	1	0
414 
-chr12	125024291	125024291	100	1	0
415 
-chr12	125024320	125024320	100	1	0
416 
-chr12	125024325	125024325	100	1	0
417 
-chr12	126019538	126019538	0	0	1
418 
-chr12	127965960	127965960	100	1	0
419 
-chr12	127965981	127965981	100	1	0
420 
-chr12	128524899	128524899	0	0	1
421 
-chr12	128932866	128932866	0	0	1
422 
-chr12	129092985	129092985	100	1	0
423 
-chr12	130746495	130746495	100	1	0
424 
-chr12	130820411	130820411	0	0	1
425 
-chr12	130820424	130820424	0	0	1
426 
-chr12	132849693	132849693	100	1	0
427 
-chr12	133386909	133386909	100	1	0
428 
-chr12	133386931	133386931	100	1	0
429 
-chr12	133386939	133386939	100	1	0
430 
-chr12	133811398	133811398	100	1	0
431 
-chr13	21949647	21949647	100	1	0
432 
-chr13	22791456	22791456	100	1	0
433 
-chr13	31542011	31542011	100	1	0
434 
-chr13	31542030	31542030	0	0	1
435 
-chr13	31609764	31609764	100	1	0
436 
-chr13	31609776	31609776	0	0	1
437 
-chr13	31609786	31609786	0	0	1
438 
-chr13	34986877	34986877	100	1	0
439 
-chr13	36120473	36120473	0	0	1
440 
-chr13	37437159	37437159	100	1	0
441 
-chr13	39437477	39437477	100	1	0
442 
-chr13	40575911	40575911	100	1	0
443 
-chr13	52059510	52059510	100	1	0
444 
-chr13	52156954	52156954	100	1	0
445 
-chr13	56314754	56314754	0	0	1
446 
-chr13	62256082	62256082	0	0	1
447 
-chr13	66103889	66103889	0	0	1
448 
-chr13	70699163	70699163	100	1	0
449 
-chr13	70699188	70699188	0	0	1
450 
-chr13	74156522	74156522	100	1	0
451 
-chr13	80246646	80246646	0	0	1
452 
-chr13	80934105	80934105	100	1	0
453 
-chr13	82444385	82444385	0	0	1
454 
-chr13	82444418	82444418	0	0	1
455 
-chr13	83461872	83461872	100	1	0
456 
-chr13	83461891	83461891	100	1	0
457 
-chr13	83690966	83690966	0	0	1
458 
-chr13	83690994	83690994	100	1	0
459 
-chr13	89518708	89518708	0	0	1
460 
-chr13	93580213	93580213	100	1	0
461 
-chr13	98211829	98211829	100	1	0
462 
-chr13	101096027	101096027	100	1	0
463 
-chr13	101613765	101613765	100	1	0
464 
-chr13	101763479	101763479	100	1	0
465 
-chr13	101763488	101763488	100	1	0
466 
-chr13	102459385	102459385	100	1	0
467 
-chr13	104989341	104989341	100	1	0
468 
-chr13	104989345	104989345	100	1	0
469 
-chr13	104989358	104989358	100	1	0
470 
-chr13	106093149	106093149	100	1	0
471 
-chr13	106234396	106234396	0	0	1
472 
-chr13	106850352	106850352	100	1	0
473 
-chr13	109054306	109054306	0	0	1
474 
-chr13	109054341	109054341	0	0	1
475 
-chr13	111277242	111277242	100	1	0
476 
-chr13	111277246	111277246	100	1	0
477 
-chr13	111277288	111277288	100	1	0
478 
-chr13	112872123	112872123	100	1	0
479 
-chr13	113799168	113799168	100	1	0
480 
-chr13	113799172	113799172	100	1	0
481 
-chr13	113799176	113799176	0	0	1
482 
-chr13	113799185	113799185	100	1	0
483 
-chr13	113855775	113855775	100	1	0
484 
-chr14	20928153	20928153	100	1	0
485 
-chr14	20928158	20928158	100	1	0
486 
-chr14	20928193	20928193	100	1	0
487 
-chr14	22953423	22953423	100	1	0
488 
-chr14	36154145	36154145	100	1	0
489 
-chr14	36154164	36154164	100	1	0
490 
-chr14	37166364	37166364	100	1	0
491 
-chr14	37740210	37740210	100	1	0
492 
-chr14	37740216	37740216	100	1	0
493 
-chr14	38605480	38605480	0	0	1
494 
-chr14	39161001	39161001	100	1	0
495 
-chr14	39843975	39843975	100	1	0
496 
-chr14	40149063	40149063	100	1	0
497 
-chr14	43808278	43808278	0	0	1
498 
-chr14	45405980	45405980	100	1	0
499 
-chr14	45406013	45406013	100	1	0
500 
-chr14	46012695	46012695	0	0	1
501 
-chr14	46091134	46091134	0	0	1
502 
-chr14	46096138	46096138	0	0	1
503 
-chr14	46319443	46319443	0	0	1
504 
-chr14	48088540	48088540	0	0	1
505 
-chr14	48346726	48346726	100	1	0
506 
-chr14	49964016	49964016	0	0	1
507 
-chr14	56476266	56476266	100	1	0
508 
-chr14	57058501	57058501	100	1	0
509 
-chr14	57501294	57501294	0	0	1
510 
-chr14	60672128	60672128	100	1	0
511 
-chr14	66292930	66292930	100	1	0
512 
-chr14	66429875	66429875	0	0	1
513 
-chr14	66727906	66727906	0	0	1
514 
-chr14	68369076	68369076	100	1	0
515 
-chr14	68496269	68496269	100	1	0
516 
-chr14	68953969	68953969	100	1	0
517 
-chr14	70398818	70398818	100	1	0
518 
-chr14	76637724	76637724	0	0	1
519 
-chr14	76637746	76637746	0	0	1
520 
-chr14	76978027	76978027	0	0	1
521 
-chr14	81187394	81187394	100	1	0
522 
-chr14	84321905	84321905	100	1	0
523 
-chr14	84868009	84868009	0	0	1
524 
-chr14	85793723	85793723	100	1	0
525 
-chr14	86169713	86169713	100	1	0
526 
-chr14	89704679	89704679	100	1	0
527 
-chr14	90985236	90985236	100	1	0
528 
-chr14	90985244	90985244	100	1	0
529 
-chr14	91797186	91797186	0	0	1
530 
-chr14	93902116	93902116	0	0	1
531 
-chr14	96770757	96770757	100	1	0
532 
-chr14	96804458	96804458	100	1	0
533 
-chr14	96804464	96804464	100	1	0
534 
-chr14	97057587	97057587	0	0	1
535 
-chr14	97266793	97266793	100	1	0
536 
-chr14	97266797	97266797	100	1	0
537 
-chr14	101626825	101626825	100	1	0
538 
-chr14	101642843	101642843	100	1	0
539 
-chr14	101642870	101642870	100	1	0
540 
-chr14	104139938	104139938	100	1	0
541 
-chr14	104733695	104733695	0	0	1
542 
-chr14	104733707	104733707	0	0	1
543 
-chr14	104733725	104733725	0	0	1
544 
-chr14	105074332	105074332	100	1	0
545 
-chr14	105379367	105379367	100	1	0
546 
-chr14	105379375	105379375	100	1	0
547 
-chr14	106832960	106832960	0	0	1
548 
-chr15	20463913	20463913	0	0	1
549 
-chr15	22971122	22971122	100	1	0
550 
-chr15	22971148	22971148	100	1	0
551 
-chr15	26402476	26402476	0	0	1
552 
-chr15	29155788	29155788	0	0	1
553 
-chr15	29366250	29366250	100	1	0
554 
-chr15	33321087	33321087	100	1	0
555 
-chr15	33321090	33321090	100	1	0
556 
-chr15	36616034	36616034	100	1	0
557 
-chr15	37640617	37640617	100	1	0
558 
-chr15	37640656	37640656	100	1	0
559 
-chr15	43536915	43536915	0	0	1
560 
-chr15	45214442	45214442	100	1	0
561 
-chr15	45780005	45780005	100	1	0
562 
-chr15	47192259	47192259	100	1	0
563 
-chr15	48543160	48543160	100	1	0
564 
-chr15	48543164	48543164	0	0	1
565 
-chr15	51066524	51066524	100	1	0
566 
-chr15	51066532	51066532	100	1	0
567 
-chr15	53011955	53011955	0	0	1
568 
-chr15	56090979	56090979	0	0	1
569 
-chr15	57613029	57613029	0	0	1
570 
-chr15	57613043	57613043	0	0	1
571 
-chr15	57613046	57613046	0	0	1
572 
-chr15	57629868	57629868	100	1	0
573 
-chr15	58406713	58406713	0	0	1
574 
-chr15	60838192	60838192	100	1	0
575 
-chr15	61027720	61027720	100	1	0
576 
-chr15	62221081	62221081	0	0	1
577 
-chr15	62876681	62876681	100	1	0
578 
-chr15	67058858	67058858	100	1	0
579 
-chr15	67950450	67950450	100	1	0
580 
-chr15	70419745	70419745	0	0	1
581 
-chr15	70688129	70688129	100	1	0
582 
-chr15	72456520	72456520	100	1	0
583 
-chr15	72851901	72851901	100	1	0
584 
-chr15	73999579	73999579	100	1	0
585 
-chr15	74902976	74902976	0	0	1
586 
-chr15	75644025	75644025	100	1	0
587 
-chr15	77544387	77544387	100	1	0
588 
-chr15	79079722	79079722	100	1	0
589 
-chr15	79079736	79079736	100	1	0
590 
-chr15	80729189	80729189	0	0	1
591 
-chr15	81045768	81045768	0	0	1
592 
-chr15	81045799	81045799	100	1	0
593 
-chr15	83479487	83479487	0	0	1
594 
-chr15	83479490	83479490	0	0	1
595 
-chr15	87457861	87457861	0	0	1
596 
-chr15	90414506	90414506	100	1	0
597 
-chr15	90506981	90506981	100	1	0
598 
-chr15	91403176	91403176	100	1	0
599 
-chr15	92573711	92573711	100	1	0
600 
-chr15	95590603	95590603	100	1	0
601 
-chr15	95980252	95980252	100	1	0
602 
-chr15	95980285	95980285	100	1	0
603 
-chr15	98759704	98759704	0	0	1
604 
-chr15	100864591	100864591	100	1	0
605 
-chr15	101685180	101685180	100	1	0
606 
-chr15	101685188	101685188	0	0	1
607 
-chr15	102344300	102344300	100	1	0
608 
-chr16	272347	272347	0	0	1
609 
-chr16	1380361	1380361	100	1	0
610 
-chr16	1380383	1380383	100	1	0
611 
-chr16	1452555	1452555	100	1	0
612 
-chr16	1452570	1452570	100	1	0
613 
-chr16	1452579	1452579	100	1	0
614 
-chr16	1452598	1452598	100	1	0
615 
-chr16	1875920	1875920	100	1	0
616 
-chr16	1875932	1875932	0	0	1
617 
-chr16	1875963	1875963	0	0	1
618 
-chr16	3002568	3002568	0	0	1
619 
-chr16	3886864	3886864	100	1	0
620 
-chr16	4391401	4391401	100	1	0
621 
-chr16	4900620	4900620	100	1	0
622 
-chr16	4900643	4900643	100	1	0
623 
-chr16	5068984	5068984	0	0	1
624 
-chr16	5561008	5561008	100	1	0
625 
-chr16	6505382	6505382	0	0	1
626 
-chr16	6505386	6505386	0	0	1
627 
-chr16	7034562	7034562	0	0	1
628 
-chr16	9934864	9934864	0	0	1
629 
-chr16	10976149	10976149	100	1	0
630 
-chr16	11920397	11920397	100	1	0
631 
-chr16	11920412	11920412	100	1	0
632 
-chr16	13536923	13536923	0	0	1
633 
-chr16	15688024	15688024	0	0	1
634 
-chr16	15688027	15688027	100	1	0
635 
-chr16	18038618	18038618	0	0	1
636 
-chr16	19665701	19665701	100	1	0
637 
-chr16	22706378	22706378	0	0	1
638 
-chr16	26247168	26247168	0	0	1
639 
-chr16	26346945	26346945	100	1	0
640 
-chr16	26508483	26508483	0	0	1
641 
-chr16	26669146	26669146	0	0	1
642 
-chr16	29803189	29803189	0	0	1
643 
-chr16	29803206	29803206	100	1	0
644 
-chr16	46435497	46435497	100	1	0
645 
-chr16	46435510	46435510	100	1	0
646 
-chr16	46437963	46437963	0	0	1
647 
-chr16	50892643	50892643	100	1	0
648 
-chr16	55302268	55302268	0	0	1
649 
-chr16	56840437	56840437	100	1	0
650 
-chr16	59293266	59293266	100	1	0
651 
-chr16	59850715	59850715	0	0	1
652 
-chr16	60474865	60474865	0	0	1
653 
-chr16	60703935	60703935	100	1	0
654 
-chr16	62044345	62044345	100	1	0
655 
-chr16	63594233	63594233	0	0	1
656 
-chr16	64718121	64718121	100	1	0
657 
-chr16	67303630	67303630	100	1	0
658 
-chr16	70320602	70320602	100	1	0
659 
-chr16	70320617	70320617	100	1	0
660 
-chr16	71733230	71733230	100	1	0
661 
-chr16	72835461	72835461	100	1	0
662 
-chr16	73305557	73305557	100	1	0
663 
-chr16	75458208	75458208	100	1	0
664 
-chr16	76099551	76099551	0	0	1
665 
-chr16	76310877	76310877	0	0	1
666 
-chr16	78045070	78045070	100	1	0
667 
-chr16	78234652	78234652	100	1	0
668 
-chr16	78325163	78325163	100	1	0
669 
-chr16	80865678	80865678	100	1	0
670 
-chr16	80865701	80865701	100	1	0
671 
-chr16	80865708	80865708	100	1	0
672 
-chr16	82692792	82692792	100	1	0
673 
-chr16	83123288	83123288	100	1	0
674 
-chr16	83123326	83123326	100	1	0
675 
-chr16	83320766	83320766	100	1	0
676 
-chr16	84411211	84411211	100	1	0
677 
-chr16	85458203	85458203	0	0	1
678 
-chr16	85643120	85643120	0	0	1
679 
-chr16	85643143	85643143	100	1	0
680 
-chr16	86903252	86903252	100	1	0
681 
-chr16	89628230	89628230	0	0	1
682 
-chr17	125481	125481	100	1	0
683 
-chr17	5188120	5188120	100	1	0
684 
-chr17	5839545	5839545	0	0	1
685 
-chr17	7844459	7844459	100	1	0
686 
-chr17	11812759	11812759	0	0	1
687 
-chr17	12301341	12301341	100	1	0
688 
-chr17	12434428	12434428	100	1	0
689 
-chr17	14431675	14431675	0	0	1
690 
-chr17	15777959	15777959	100	1	0
691 
-chr17	17980682	17980682	100	1	0
692 
-chr17	19400339	19400339	100	1	0
693 
-chr17	19400368	19400368	0	0	1
694 
-chr17	21303731	21303731	0	0	1
695 
-chr17	21303751	21303751	100	1	0
696 
-chr17	26283952	26283952	0	0	1
697 
-chr17	28822191	28822191	100	1	0
698 
-chr17	28822199	28822199	100	1	0
699 
-chr17	30001712	30001712	0	0	1
700 
-chr17	31104680	31104680	100	1	0
701 
-chr17	31104684	31104684	100	1	0
702 
-chr17	31104688	31104688	100	1	0
703 
-chr17	31104690	31104690	100	1	0
704 
-chr17	31767160	31767160	100	1	0
705 
-chr17	35535851	35535851	100	1	0
706 
-chr17	36811956	36811956	0	0	1
707 
-chr17	36811987	36811987	100	1	0
708 
-chr17	37304493	37304493	100	1	0
709 
-chr17	38769181	38769181	100	1	0
710 
-chr17	38769199	38769199	0	0	1
711 
-chr17	38780007	38780007	0	0	1
712 
-chr17	38780043	38780043	100	1	0
713 
-chr17	41461222	41461222	100	1	0
714 
-chr17	41461237	41461237	100	1	0
715 
-chr17	42335983	42335983	0	0	1
716 
-chr17	42336021	42336021	100	1	0
717 
-chr17	42336029	42336029	0	0	1
718 
-chr17	42865364	42865364	100	1	0
719 
-chr17	43873195	43873195	100	1	0
720 
-chr17	43873201	43873201	100	1	0
721 
-chr17	44855129	44855129	0	0	1
722 
-chr17	46225004	46225004	100	1	0
723 
-chr17	48673023	48673023	100	1	0
724 
-chr17	48673036	48673036	100	1	0
725 
-chr17	51873879	51873879	0	0	1
726 
-chr17	54208766	54208766	100	1	0
727 
-chr17	54407106	54407106	100	1	0
728 
-chr17	55710485	55710485	100	1	0
729 
-chr17	59140081	59140081	100	1	0
730 
-chr17	59364702	59364702	100	1	0
731 
-chr17	63693310	63693310	100	1	0
732 
-chr17	63693352	63693352	0	0	1
733 
-chr17	65489307	65489307	100	1	0
734 
-chr17	65970949	65970949	100	1	0
735 
-chr17	65970955	65970955	100	1	0
736 
-chr17	65970988	65970988	100	1	0
737 
-chr17	70514268	70514268	100	1	0
738 
-chr17	71539612	71539612	0	0	1
739 
-chr17	74415093	74415093	100	1	0
740 
-chr17	74415101	74415101	100	1	0
741 
-chr17	74415103	74415103	100	1	0
742 
-chr17	74464093	74464093	0	0	1
743 
-chr17	74852242	74852242	0	0	1
744 
-chr17	75355107	75355107	100	1	0
745 
-chr17	75792348	75792348	0	0	1
746 
-chr17	80434475	80434475	100	1	0
747 
-chr18	318963	318963	100	1	0
748 
-chr18	318970	318970	100	1	0
749 
-chr18	930289	930289	0	0	1
750 
-chr18	3804919	3804919	100	1	0
751 
-chr18	4999317	4999317	100	1	0
752 
-chr18	5791123	5791123	0	0	1
753 
-chr18	6667918	6667918	100	1	0
754 
-chr18	7243197	7243197	100	1	0
755 
-chr18	7243215	7243215	100	1	0
756 
-chr18	7243240	7243240	100	1	0
757 
-chr18	8255149	8255149	100	1	0
758 
-chr18	9436445	9436445	0	0	1
759 
-chr18	9498459	9498459	100	1	0
760 
-chr18	11389594	11389594	100	1	0
761 
-chr18	11389599	11389599	0	0	1
762 
-chr18	11389609	11389609	100	1	0
763 
-chr18	18511417	18511417	100	1	0
764 
-chr18	20816943	20816943	100	1	0
765 
-chr18	20816973	20816973	100	1	0
766 
-chr18	20816978	20816978	100	1	0
767 
-chr18	24103202	24103202	100	1	0
768 
-chr18	25718176	25718176	100	1	0
769 
-chr18	27575441	27575441	100	1	0
770 
-chr18	34770476	34770476	100	1	0
771 
-chr18	34770478	34770478	100	1	0
772 
-chr18	34770494	34770494	0	0	1
773 
-chr18	34827148	34827148	0	0	1
774 
-chr18	35362192	35362192	100	1	0
775 
-chr18	37806685	37806685	0	0	1
776 
-chr18	39836590	39836590	0	0	1
777 
-chr18	42283603	42283603	100	1	0
778 
-chr18	42555385	42555385	0	0	1
779 
-chr18	44153219	44153219	0	0	1
780 
-chr18	44153232	44153232	0	0	1
781 
-chr18	44427810	44427810	100	1	0
782 
-chr18	46159127	46159127	100	1	0
783 
-chr18	46603812	46603812	100	1	0
784 
-chr18	48190221	48190221	0	0	1
785 
-chr18	50928307	50928307	0	0	1
786 
-chr18	51132705	51132705	0	0	1
787 
-chr18	51602931	51602931	100	1	0
788 
-chr18	52490415	52490415	0	0	1
789 
-chr18	55793417	55793417	100	1	0
790 
-chr18	60382351	60382351	0	0	1
791 
-chr18	60382353	60382353	0	0	1
792 
-chr18	60382355	60382355	0	0	1
793 
-chr18	60382357	60382357	0	0	1
794 
-chr18	60382360	60382360	0	0	1
795 
-chr18	60382379	60382379	0	0	1
796 
-chr18	60382385	60382385	0	0	1
797 
-chr18	60458241	60458241	100	1	0
798 
-chr18	60458265	60458265	100	1	0
799 
-chr18	61313461	61313461	0	0	1
800 
-chr18	61313465	61313465	0	0	1
801 
-chr18	61611568	61611568	100	1	0
802 
-chr18	61611574	61611574	100	1	0
803 
-chr18	65514853	65514853	100	1	0
804 
-chr18	65514860	65514860	100	1	0
805 
-chr18	65848507	65848507	100	1	0
806 
-chr18	65848528	65848528	100	1	0
807 
-chr18	67692953	67692953	0	0	1
808 
-chr18	68317966	68317966	100	1	0
809 
-chr18	68497743	68497743	0	0	1
810 
-chr18	71071990	71071990	100	1	0
811 
-chr18	71263127	71263127	100	1	0
812 
-chr18	73324156	73324156	100	1	0
813 
-chr18	73458416	73458416	0	0	1
814 
-chr18	74335075	74335075	100	1	0
815 
-chr18	75445617	75445617	100	1	0
816 
-chr18	75445657	75445657	0	0	1
817 
-chr18	77335412	77335412	100	1	0
818 
-chr18	77469723	77469723	100	1	0
819 
-chr18	77469752	77469752	100	1	0
820 
-chr19	2677288	2677288	100	1	0
821 
-chr19	2917520	2917520	100	1	0
822 
-chr19	2917526	2917526	100	1	0
823 
-chr19	4403730	4403730	0	0	1
824 
-chr19	6613615	6613615	100	1	0
825 
-chr19	7286181	7286181	0	0	1
826 
-chr19	7292475	7292475	100	1	0
827 
-chr19	7515583	7515583	100	1	0
828 
-chr19	7515589	7515589	100	1	0
829 
-chr19	7515617	7515617	100	1	0
830 
-chr19	7515623	7515623	100	1	0
831 
-chr19	9714954	9714954	100	1	0
832 
-chr19	10934189	10934189	100	1	0
833 
-chr19	15550003	15550003	100	1	0
834 
-chr19	15550021	15550021	0	0	1
835 
-chr19	21854394	21854394	0	0	1
836 
-chr19	27738478	27738478	100	1	0
837 
-chr19	27738487	27738487	100	1	0
838 
-chr19	28730092	28730092	100	1	0
839 
-chr19	29441229	29441229	100	1	0
840 
-chr19	31747232	31747232	100	1	0
841 
-chr19	31747259	31747259	100	1	0
842 
-chr19	36130836	36130836	0	0	1
843 
-chr19	38823316	38823316	100	1	0
844 
-chr19	39607335	39607335	100	1	0
845 
-chr19	39607353	39607353	100	1	0
846 
-chr19	39607370	39607370	100	1	0
847 
-chr19	41165867	41165867	100	1	0
848 
-chr19	42167798	42167798	0	0	1
849 
-chr19	42407035	42407035	100	1	0
850 
-chr19	42407053	42407053	100	1	0
851 
-chr19	42407055	42407055	100	1	0
852 
-chr19	43815943	43815943	0	0	1
853 
-chr19	43901277	43901277	100	1	0
854 
-chr19	47373066	47373066	100	1	0
855 
-chr19	48540038	48540038	0	0	1
856 
-chr19	49422176	49422176	0	0	1
857 
-chr19	50170448	50170448	100	1	0
858 
-chr19	50170458	50170458	100	1	0
859 
-chr19	50437091	50437091	100	1	0
860 
-chr19	51737870	51737870	0	0	1
861 
-chr19	54689310	54689310	100	1	0
862 
-chr19	57067941	57067941	100	1	0
863 
-chr19	59045293	59045293	100	1	0
864 
-chr2	35131	35131	0	0	1
865 
-chr2	2747988	2747988	0	0	1
866 
-chr2	3296505	3296505	100	1	0
867 
-chr2	5507761	5507761	0	0	1
868 
-chr2	6611207	6611207	0	0	1
869 
-chr2	10166599	10166599	100	1	0
870 
-chr2	10266862	10266862	0	0	1
871 
-chr2	14259811	14259811	100	1	0
872 
-chr2	15019066	15019066	100	1	0
873 
-chr2	16767788	16767788	100	1	0
874 
-chr2	18502370	18502370	0	0	1
875 
-chr2	19915059	19915059	100	1	0
876 
-chr2	22366093	22366093	100	1	0
877 
-chr2	22366122	22366122	0	0	1
878 
-chr2	24719999	24719999	100	1	0
879 
-chr2	29259464	29259464	100	1	0
880 
-chr2	29864190	29864190	100	1	0
881 
-chr2	31738850	31738850	100	1	0
882 
-chr2	34802457	34802457	0	0	1
883 
-chr2	35772135	35772135	100	1	0
884 
-chr2	36739200	36739200	100	1	0
885 
-chr2	36966725	36966725	100	1	0
886 
-chr2	38566509	38566509	100	1	0
887 
-chr2	38566514	38566514	100	1	0
888 
-chr2	39536421	39536421	100	1	0
889 
-chr2	43211594	43211594	100	1	0
890 
-chr2	43833593	43833593	0	0	1
891 
-chr2	44456235	44456235	100	1	0
892 
-chr2	44456247	44456247	100	1	0
893 
-chr2	44456269	44456269	100	1	0
894 
-chr2	45944695	45944695	0	0	1
895 
-chr2	47510047	47510047	100	1	0
896 
-chr2	49251434	49251434	0	0	1
897 
-chr2	49790156	49790156	0	0	1
898 
-chr2	60691638	60691638	100	1	0
899 
-chr2	61852915	61852915	0	0	1
900 
-chr2	61852931	61852931	100	1	0
901 
-chr2	64426585	64426585	100	1	0
902 
-chr2	66810842	66810842	0	0	1
903 
-chr2	66810844	66810844	0	0	1
904 
-chr2	66810851	66810851	0	0	1
905 
-chr2	70639155	70639155	100	2	0
906 
-chr2	71138824	71138824	100	1	0
907 
-chr2	73908500	73908500	0	0	1
908 
-chr2	74379461	74379461	100	1	0
909 
-chr2	86334315	86334315	0	0	1
910 
-chr2	86334332	86334332	0	0	1
911 
-chr2	89867998	89867998	100	1	0
912 
-chr2	89878959	89878959	0	0	1
913 
-chr2	89878990	89878990	0	0	1
914 
-chr2	92317773	92317773	0	0	1
915 
-chr2	95653129	95653129	100	1	0
916 
-chr2	95653169	95653169	0	0	1
917 
-chr2	97009009	97009009	100	1	0
918 
-chr2	99014228	99014228	0	0	1
919 
-chr2	99310922	99310922	0	0	1
920 
-chr2	99546323	99546323	100	1	0
921 
-chr2	100815719	100815719	100	1	0
922 
-chr2	101450379	101450379	100	1	0
923 
-chr2	102208357	102208357	100	1	0
924 
-chr2	102902067	102902067	100	1	0
925 
-chr2	105531329	105531329	0	0	1
926 
-chr2	107472828	107472828	0	0	1
927 
-chr2	109557597	109557597	100	1	0
928 
-chr2	109557603	109557603	100	1	0
929 
-chr2	111986397	111986397	100	1	0
930 
-chr2	111988014	111988014	100	1	0
931 
-chr2	112596031	112596031	100	1	0
932 
-chr2	112596053	112596053	100	1	0
933 
-chr2	113075985	113075985	100	1	0
934 
-chr2	113518929	113518929	100	1	0
935 
-chr2	113518953	113518953	100	1	0
936 
-chr2	114561479	114561479	100	1	0
937