NEWS

BeadDataPackR 1.5

Beads with negative coordinates can now be included in the bab file
If overlapping segments are found a warning is printed and the full locs index is used.
Coordinate values returned by readCompressedData() are now rounded to match the precision of the original text file.

Improved performance of readCompressedData() when extracting all probeIDs.
Fixed error when a vector of files was passed to decompressBeadData(). Formerly, if arrayMask was NULL each output file was created with the same name, overwriting the previous one.

Moved example data to inst/extdata in accordance with R pacakge guidelines. Removes warning from R CMD check.

Added function extractLocsFile()
Added function readCompressedData()
decompressBeadData() will now take a vector of input files, rather than requiring a loop.
Reduced decompression time by about 50% by using .Call() rather than apply()

Fixed error when extracting red channel information using readCompressedData(). Thanks to Prof. Tim Triche for identifying and patching this.
Fixed rounding errors when dealing with very small and/or negative coordinates.
Check indices are now employed correctly.
If any beads can't be positioned using the reduced index compression halts and the user is informed.
Fixed a major bug that resulted in the .locs file being randomly ordered on reconstruction if the full index was used.
Now stops and informs the user if there are negative coordinates in the .locs file.

Improved speed when using lossy compression by switcing some code from apply() to .Call()
Progress bar is now optional
Package created

Fixed bug which put red channel out by 1 pixel when using offset coordinates
Now works correctly in the case where an array consists of a single segment, e.g. Human 1M
Fixed bug in creating full index
Fixed bug in combining .txt and .locs files due to duplicate entries
Fixed bug in writing intensity flags. Introduced when switching from calloc() to R_alloc().
Set a default file name for output from compressBeadData if left blank
Compression progress bar no longer stops at 70%
Set limits on the number of bytes for storing the fractional part
Replaced calloc() with R_alloc() in C code
Registered C functions