Lightning

h1. cgb

@cgb@ is a tool to help with access to the binary compact genome format (CGF).  The tool is still in the prototyping stage.

Code for @cgb@ can be found on [github.com/abeconnelly/cgf](https://github.com/abeconnelly/cgf).

h2. Quick start

<pre>

$ git clone https://github.com/abeconnelly/cgf

$ cd cgf/cpp

$ ./cmp.sh

$ ./cgb -i data/hu826751-GS03052-DNA_B01.cgf -s 0 -B -k -p 862

[ 79 8 0 0 0 0 0 -1 0 0 0 389 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 -1 34 -1 185 1]

[ 79 2 0 0 0 0 0 -1 0 0 0 390 0 0 0 0 0 1 0 0 0 0 0 0 26 0 0 1 0 0 -1 34 -1 185 1]

[[ ][ ][ ][ ][ ][ ][ 903 1 ][ ][ 16 1 ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ 96 1 ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ 291 2 ]]

[[ ][ ][ ][ ][ ][ ][ 903 1 ][ ][ 16 1 ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ 96 1 ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ 291 2 ]]

</pre>

h2. Brief overview

@cgb@ is meant to help debug and inspect CGF files.  The two main features are to report the contents of a CGF in terms of tile variants and low quality information as well as to do some basic tile concordance operations.  The code that @cgb@ uses is shared by the Lightning CGF server and is in part meant to test functionality used there.

h3. Concordance

The CGF has different 'tiers' of information, from a bit vector representing whether the tile is canonical, to a cache holding the first 8 tile variants to the overflow tables if the cache is exceeded.  To test and for rough estimates, different 'levels' of concordance are used with @cgb@.

* Level 0 - compare canonical tiles only

* Level 1 - compare canonical tiles and cache

* Level 2 - a full tile concordance

h5. example

<pre>

$ ./cgb -i data/hu826751-GS03052-DNA_B01.cgf -i data/hg19.cgf -l 0

level: 0, canonical match: 6491163

$ ./cgb -i data/hu826751-GS03052-DNA_B01.cgf -i data/hg19.cgf -l 1

level: 1, canonical+cache match: 6519788, loq: 148760

$ ./cgb -i data/hu826751-GS03052-DNA_B01.cgf -i data/hg19.cgf -l 2

#match_tot: 6610685

</pre>

h3. CGF Inspection

h5. JSON Tile Path information

Get tile path 862 (0x35e, which is chrM) starting at tile 0 including low quality information and print in JSON format.

<pre>

$ ./cgb -i data/hu826751-GS03052-DNA_B01.cgf -p 862 -s 0 -B

{

  "035e":{

    "tilepath":862,

    "start_tilestep":0,

    "allele":[

      [ 79, 8, 0, 0, 0, 0, 0, -1, 0, 0, 0, 389, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, -1, 34, 

      -1, 185, 1 ],

      [ 79, 2, 0, 0, 0, 0, 0, -1, 0, 0, 0, 390, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 26, 0, 0, 1, 0, 0, -1, 34, 

      -1, 185, 1 ]

    ],

    "loq_info":[

      [ [ ], [ ], [ ], [ ], [ ], [ ], [ 903, 1 ], [ ], [ 16, 1 ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ 96, 1 ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], 

        [ ], [ ], [ 291, 2 ] ],

      [ [ ], [ ], [ ], [ ], [ ], [ ], [ 903, 1 ], [ ], [ 16, 1 ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ 96, 1 ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], [ ], 

        [ ], [ ], [ 291, 2 ] ]

    ]

  }

}

</pre>

h5. Tile Path Compact Representation

Get tile path 862 (0x35e, which is chrM) starting at tile 0 including low quality information

<pre>

$ ./cgb -i data/hu826751-GS03052-DNA_B01.cgf -p 862 -s 0 -B -L -k

[ 79 8 0 0 0 0 0 -1 0 0 0 389 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 -1 34 -1 185 1]

[ 79 2 0 0 0 0 0 -1 0 0 0 390 0 0 0 0 0 1 0 0 0 0 0 0 26 0 0 1 0 0 -1 34 -1 185 1]

[[ ][ ][ ][ ][ ][ ][ 903 1 ][ ][ 16 1 ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ 96 1 ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ 291 2 ]]

[[ ][ ][ ][ ][ ][ ][ 903 1 ][ ][ 16 1 ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ 96 1 ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ ][ 291 2 ]]

</pre>

h5. Inspect Binary File (Debug)

Get a debugging printout of the information in the CGF file

<pre>

$ ./cgb -i data/hu826751-GS03052-DNA_B01.cgf -D -i data/hg19.cgf

Magic: "cgf.b"{ (7b22622e66676322)

CGFVersion: 0.1.0

LibVersion: 0.1.0

PathCount: 863

TileMapLength: 7044

TileMap:

   [[0+1],[0+1]], [[0+1],[1+1]], [[1+1],[0+1]], [[1+1],[1+1]], [[0+1],[2+1]], [[2+1],[0+1]], [[0+1,0+1],[1+2]], [[1+2],[0+1,0+1]], [[0+2],[0+2]], [[0+1],[3+1]], [[3+1],[0+1]], [[1+1,0+1],[0+2]], [[0+2],[1+1,0+1]], [[0+1],[4+1]], [[4+1],[0+1]], [[1+2],[1+2]], [[2+1],[2+1]], [[1+1],[3+1]], [[3+1],[1+1]], [[1+1],[2+1]], [[2+1],[1+1]], [[0+1],[5+1]], [[5+1],[0+1]], [[0+1],[6+1]], [[6+1],[0+1]], [[0+1,0+1],[2+2]], [[2+2],[0+1,0+1]], [[0+1,0+1],[3+2]], [[3+2],[0+1,0+1]], [[3+1],[3+1]], [[0+1],[7+1]], [[7+1],[0+1]],

...

  035e.Loq.LoqFlagByteCount: 5

  035e.Loq.LoqFlag[5]:

     40 01 20 00 04

  035e.Loq.LoqInfoByteCount: 18

  035e.Loq.LoqInfo[18]:

     01 02 83 87 01 01 02 10 01 01 02 60 01 01 02 81 23 02

</pre>