/usr/lib/R/site-library/rtracklayer/NEWS is in r-bioc-rtracklayer 1.38.0-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 | CHANGES IN VERSION 1.30
-----------------------
NEW FEATURES
o Add readGFF(), a fast and flexible GFF/GTF parser implemented in C. See
?readGFF for more information.
SIGNIFICANT USER-VISIBLE CHANGES
o import.gff() now uses readGFF() internally which makes it at least 5x
faster in most use cases and dramatically reduces its memory footprint.
CHANGES IN VERSION 1.26
-----------------------
NEW FEATURES
o ucscGenomes() retrieves organism information
o New function exportToTabix() exports a GRanges to a
tabix-indexed tab separated file that contains all of the
metadata columns. Use import,TabixFile to load specific ranges
of data back into a GRanges.
o BigWig import/export to/from Integer/Numeric/RleList is now much
more efficient, and uses a more efficient storage format within
the BigWig file, when possible.
SIGNIFICANT USER-VISIBLE CHANGES
o BSgenome export methods are now in BSgenome.
BUG FIXES
o Handling of quotes in GFF3 is now consistent with the spec.
CHANGES IN VERSION 1.22
-----------------------
NEW FEATURES
o import,BigWigFile gains an asRle parameter that returns the data as an
RleList (assuming it tiles the sequence); much faster than importing a
GRanges and calling coverage() on it.
o add export,RleList,BigWigFile method for direct (and much more
efficient) output of RleLists (like coverage) to BigWig files.
SIGNIFICANT USER-VISIBLE CHANGES
o UCSCData now extends GRanges instead of RangedData (thanks Herve)
BUG FIXES
o handle different Set-Cookie header field casing; often due to proxies
(thanks to Altuna Akalin)
o attempt to more gracefully handle UCSC truncation of large data downloads
o handle re-directs due to UCSC mirroring (thanks Martin Morgan)
CHANGES IN VERSION 1.20
-----------------------
NEW FEATURES
o Table query interface supports multiple query ranges.
o Files (RTLFile objects) can be directly uploaded to UCSC, via track<-.
SIGNIFICANT USER-VISIBLE CHANGES
o All methods with asRangedData argument now have it default to
FALSE, instead of TRUE. A warning is issued if the argument is
missing. Eventually, we will drop all support for RangedData
import (export will still work via automatic coercion to
GRanges).
BUG FIXES
o Chromosome list for a genome is now downloaded from the table
browser, instead of the Genome Browser page. This supports
genomes with more than 1000 contigs.
o BEDX+Y formats now work when a track line is present, and the
extraCols argument is used for the column names.
o path.expand() is now called for paths passed off to the Kent library.
o Order of metadata columns upon GFF import no longer depends on LC_COLLATE.
CHANGES IN VERSION 1.17
-----------------------
NEW FEATURES
o Export of GappedAlignments objects as BAM files. There is also a
corresponding import method.
o Support for BEDX+Y import using the extraCols parameter to import.
o Direct export of RleList objects to BigWig files.
CHANGES IN VERSION 1.15
-----------------------
NEW FEATURES
o Integrated with tabix via Rsamtools. BED and GFF export methods
now generate a tabix index, if index=TRUE. Most import() methods
gain a 'which' argument that takes advantage of tabix, when
available.
o Added wigToBigWig() function for efficient conversion of WIG to BigWig.
o Added SeqinfoForBSGenome() and SeqinfoForUCSCGenome() for
conveniently retrieving Seqinfo objects for a given genome.
o Added support for FASTA import/export via Biostrings.
o GTF and GVF files are now parsed as GFF.
SIGNIFICANT USER-VISIBLE CHANGES
o The import/export API is now based on RTLFile objects, which
wrap a file path, URL or connection. There is an RTLFile
subclass for every file format. This makes it easier to extend
rtracklayer (export, import) with new file types. The existing
API is still supported (and even encouraged for most uses).
o Handle CSV attributes in GFF3 using CharacterList columns.
o BED columns thickStart/thickEnd translate to an IRanges column
named "thick". The blockStarts/Sizes/Count columns now map to a
single RangesList "blocks" column.
BUG FIXES
o Numerous fixes in the import/export methods, as a result of
implementing a full unit test suite. If something was not
working for you in the past, please try again.
o Compression and connections should now work fairly uniformly
across file types.
(start date: 29 March, 2012)
|