How to use tdf files?

[Daekyoung Jung]

Hello, there.

I am going to build a tool to visualize genome sequence, something
like igv viewer.
I tried to use .tdf files as data source, but it is hard to know where
the format is specified.
All that I can find is that .tdf files are constructed using "tile"
igvtool command from text-based files, and that they are designed for
faster processing in igv viewer. I check that the open source code of
igv, and I get the file named "notes.txt" in the folder named
"org.broad.igv.tdf", which I believe tdf converter. It saids like
this:

General layout
[Header]
[Tiles]
[Datasets]
[Groups]
[Master Index]

Header
------
magic number (32 bit int)
version (32 bit int
index position (64 bit long)
index size (bytes) (32 bit int)
header size (bytes) (32 bit int -- # of bytes for rest of header).
# of window functions
[window functions]
track type (string)
track line (string)
# of tracks
[track names]

FixedTile
---------
Type
# Positions
Start location
Span
Data

Features
---------
magic number (32 bit int) <= 'F','E', 'A', 'T'
format (string) <= bed, gff, other
[chr (string)
start (int)
rest of record (string)]

FeatureIndex
------------

Dataset
-------
# attributes
[attribute key (string)
attribute value (string]
data type
tile width
# tiles
[tile position
tile size (bytes)] <= THIS IS NOT NECCESSARY

Group
------
# attributes
[attribute key (string)
attribute value (string]

Master Index
-----------
feature index position (long) (-1 if no features)
# datasets
[dataset name (string)
position (long)
size in bytes (int)] <= THIS IS NOT NECCESSARY
# groups
[group name
position (long)
size in bytes (int)] <= THIS IS NOT NECCESSARY

seek(long position)
read(buffer, offset, length)
length() <== Only used for testing end of file

I think this specification does not include some information. For
example how many bit is needed to represent "# of window functions"?
Can anyone have the whole specification of tdf file format? Then
please let me know it.

Thank you.

[Jim Robinson]

Hi,

We have not published "tdf" yet, we might do so in the future but for
the time being the only specification available is the source code.

best,

Jim