
This hybrid version of samtools is essentially samtools version 
0.1.7a (r510), except the 0.1.7a bgzf logic and "calmd" functionality 
have been replaced with the bgzf and "calmd" from samtools version 
0.1.12a (r862).

The purpose is to provide in one executable Heng Li's BAQ base 
call quality score adjustment functionality from "calmd", as well 
as to output valid .glf format when using 'samtools pileup -g'.  
This hybrid version does not provide the samtools "mpileup" SNP 
calling capability, nor the "idxstats" and "reheader" capabilities 
that are present in the full version 0.1.12a.

Updated files:
   bamtk.c        - updated PACKAGE_VERSION to read "0.1.7-hybrid (r510 + r862)"
                    updated the description for calmd
   bam_md.c       - replaced with the version from 0.1.12a
                    and added -C to calmd usage note
   kprobaln.h     - added the version from 0.1.12a
   kprobaln.c     - added the version from 0.1.12a
   Makefile       - updated to:
                       include kprobaln.o
                       name the executable samtools-hybrid instead of samtools
   ChangeLog      - replaced with the version from 0.1.12a
   NEWS           - replaced with the version from 0.1.12a
   HYBRID_VERSION - new file describing the changes for this version.
   
The other purpose of this hybrid version is to include the latest version of
the logic used in the StatGen library, while still supporting 'pileup -g'.

The StatGen Library uses bgzf from samtools for reading and writing files 
in that format.  The bgzf logic uses the following files:
   bgzf.h         - updated to the version from 0.1.12a
   khash.h        - has not changed between 0.1.7a and 0.1.12a
   knetfile.h     - has not changed between 0.1.7a and 0.1.12a
   bgzf.c         - updated to the version from 0.1.12a
   knetfile.c     - updated to the version from 0.1.12a
These files should be kept up to date with the latest version of samtools 
so the latest set of updates are included by the StatGen library.

The StatGen Library also uses bam_reg2bin from bam.h.  Since the method 
was not changed between 0.1.7a and 0.1.12a, no updates were made to the 
0.1.7a version of bam.h.
   bam.h   bam_reg2bin

Mary Kate Trost
March 9, 2011
University of Michigan
