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diff --git a/html/js/base.js b/html/js/base.js
deleted file mode 100644
index 7f18720..0000000
--- a/html/js/base.js
+++ /dev/null
@@ -1,53 +0,0 @@
-
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-
-$('body').scrollspy({
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-$("li.disabled a").click(function() {
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- var scrolledToBottomOfPage = (
- (window.innerHeight + window.scrollY) >= document.body.offsetHeight
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diff --git a/html/js/bootstrap-3.0.3.min.js b/html/js/bootstrap-3.0.3.min.js
deleted file mode 100644
index 1a6258e..0000000
--- a/html/js/bootstrap-3.0.3.min.js
+++ /dev/null
@@ -1,7 +0,0 @@
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-
-
-
-
- RLEVectors
-RLEVectors is an alternate implementation of the Rle type from
-Bioconductor's IRanges package by H. Pages, P. Aboyoun and
-M. Lawrence. RLEVectors represent a vector with repeated values as the
-ordered set of values and repeat extents. In the field of genomics,
-data of various types are measured across the ~3 billion letters in
-the human genome can often be represented in a few thousand runs. It
-is useful to know the bounds of genome regions covered by these runs,
-the values associated with these runs, and to be able to perform
-various mathematical operations on these values.
-
Background
-Bioconductor has some widely used and extremely convenient types for
-working with collections of ranges, which sometimes are with
-associated data.IRanges represents a collection of arbitrary start,
-end pairs in [1,Inf). GRanges uses IRanges to represent locations
-on a genome and adds annotation of the chromosome and strand for each
-range. Children of GRanges add other annotations the the ranges. Rle
-represents the range [1:n] broken into arbitrary chunks or segments.
Implementation Details
-RLEVectors differs from R's Rle in that we store the run values
-and run ends rather than the run values and run lengths. The run ends
-are convenient in that they allow for indexing into the vector by
-binary search (scalar indexing is O(log(n)) rather than O(n) ).
-Additionally, length is O(1) rather than O(n) (it's the last run
-end rather than the sum of the run lengths). On the other hand,
-various operations do require the run lengths, which have to be
-calculated. See the benchmark directory and reports to see how
-this plays out.
Creation
-RLEVectors can be created from a single vector or a vector of values and a vector of run ends. In either case runs of values or zero length runs will be compressed out. RLEVectors can be expanded to a full vector like a Range with collect.
x = RLEVector([1,1,2,2,3,3,4,4,4])
-x = RLEVector([4,5,6],[3,6,9])
-collect(x)
Describing
-RLEVectors implement the standard Vector API and also other methods for describing the ranges and values:
--
-
length(x)# The full length of the vector, uncompressed
-nrun(x)# The number of runs in the vector
-rstart(x)# The index of the beginning of each run
-rwidth(x)# The width of each run
-rstart(x)# The index of the end of each run
-
Naming for some of these functions is difficult given that many useful names are already reserved words (end, start, last). Suggestions are welcome at this stage of development.
Standard vector operations
-RLEVectors can be treated as standard Vectors for arithmetic and collection operations. In many cases these operations are more efficient than operations on a standard vector.
-
-
x = RLEVector([4,5,6],[3,6,9])
-x[2]
-x[7:9] = 10
-push!(x,6)
-x + 2x
-unique(x)
-findin(x,5)
-x > 4.2
-sort(x)
-median(x)
-
Relative speed
-RLEVectors has been extensively profiled and somewhat optimized. Please see the benchmarking section for the evolution over time and comparisons to like operations in R.
Benchmarks
-
Optimization progress
-
Memory considerations
-Data compression is a secondary benefit of RLEVectors, but it can be convenient. Generally run ends are stored as Int64. However, if further memory savings are desired, consider smaller and unsigned types. UInt32 is sufficient to hold the length of the human genome and UInt16 can hold the length of the longest human chromosome.
RLEVector([5.1,2.9,100.7], UInt16[4,8,22])
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---This software is copyright (c) by Genentech.
-Permission is hereby granted, free of charge, to any person obtaining -a copy of this software and associated documentation files (the -"Software"), to deal in the Software without restriction, including -without limitation the rights to use, copy, modify, merge, publish, -distribute, sublicense, and/or sell copies of the Software, and to -permit persons to whom the Software is furnished to do so, subject -to the following conditions:
-The above copyright notice and this permission notice shall be -included in all copies or substantial portions of the Software.
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS -BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN -ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN -CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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