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README for directory src
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This directory and its subdirectories contain the source code for TraceTuner. 

The code is supposed to be used for building the following C executables 

- ttuner                                      (subdirectory compute_qv),
- train and trainphd                          (subdirectory mktrain),
- lut                                         (subdirectory mklut),
- checkbc, checkqv, checkbcphd and checkqvphd (subdirectory mkchk), 

The executables can be used to perform the following tasks: 

- ttuner: 
  process one or more DNA traces, call (pure and/or mixed) bases from each 
  trace, evaluate quality values of all the called bases, detect 
  heterozygous indels in diploid samples and deconvolve the "mixed" 
  electropherograms containing indels into pure electropherograms corresponding
  to the long and short haplotype, and output the results in a variety of 
  formats, including many PHRED-compatible formats;

- train:
  process one or more DNA traces, call reads from the traces, evaluate four 
  predictors, or trace parameters, for each called base in a read, produce a 
  local alignment of each called read against specified correct/reference 
  sequence and output this alignment, together with the values of four 
  predictors for each called base, in a text data file;

- trainphd:
  read bases and quality values from one or more PHD files, produce a local 
  alignment of each read against specified correct/reference sequence and 
  output this alignment, together with quality value for each called base, 
  in a text data file;

- lut:
  take the alignment file produced by executable train as input and produce  
  a customized lookup tables for evaluating quality values; this table
  can be used by executable ttuner with -t option.

- checkbc and checkbcphd:
  check the accuracy of the base calls. These executables take as input
  the alignment files produced by train and trainphd, respectively;

- checkbc and checkbcphd:
  check the accuracy of quality values.
  
Each subdirectory contains its own README file which describes the usage of the
executables in more details.

To compile the source code and build the executables on Unix/Linux platform, 
type 'make". To compile the source code and build the executables in MS DOS
environment, visit every source subdirectory, starting from compute_qv,
and type 'pcmake'. 

This directory also contains Java archive file ttuner_tools.jar, which 
contains the Launcher and Viewer. These are described in the PDF file in 
directory ../doc.  The Launcher was designed for PC users so that they 
can run the basic TraceTuner options without using the MS-DOS command line.  
It may be useful on UNIX/Linux as well as it lets you select input files, 
run TraceTuner, and then immediately run the Viewer without having to specify 
paths. 

The Viewer shows the original traces, the original basecalls made by the
ABI basecaller, and the revised basecalls and quality values supplied by
TraceTuner. It requires sample file and PHD file to run.

To use the Launcher, make sure the ttuner executable is in your path so
the Launcher can find it.  Assuming Java 1.3 is in your path and that
ttuner_tools.jar file is in your current directory, the command to start
the Launcher is

    java -jar ttuner_tools.jar -Dhelpdocs.dir="$TTHOME/help"

where "TTHOME" is an environmental variable that should have been set up
properly during the installation.

To run the stand-alone Viewer on a single sample file / phd file combination
the command would be

    java -Dhelpdocs.dir="$TTHOME/help" -cp ttuner_tools.jar \
     com.paracel.tt.run.TTView <sample-file> <phd-file>

The Java tools need Java version 1.3 for the UNIX platform to be utilized.
This TraceTuner distribution does not include Java for the UNIX platforms.
If you want to use these tools on a UNIX platform, you need to download and
install the appropriate distribution from

    http://java.sun.com/

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Copyright (c) 1999-2003, Paracel, Inc.  All rights reserved.
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