
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 revision r983. 
It was originally version 0.1.12a (r862), but has since been upgraded
to r983 to bring in the enhanced BAQ logic.

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 and later.

Updated files:
   bamtk.c        - updated PACKAGE_VERSION to read "0.1.7-hybrid (r510 + r983)"
                    updated the description for calmd
   bam_md.c       - replaced with the version from r983
                    and added -C to calmd usage note
                    but hand modified to remove the definition of 
                    bam_nt16_nt4_table since in this version it is defined in
                    bam_maqcns.c
   kprobaln.h     - added the version from r983
   kprobaln.c     - added the version from r983
   Makefile       - updated to:
                       include kprobaln.o
                       name the executable samtools-hybrid instead of samtools
   ChangeLog      - replaced with the version from r983
   NEWS           - replaced with the version from r983
   HYBRID_VERSION - new file describing the changes for this version.
   
Additional Updates:
   faidx.c        - updated to the version from r983
                   (the old version failed to compile due to an
                    include that was removed from khash.h)
   

A previous purpose of this hybrid version was to include the latest version of
the logic used in the StatGen library, while still supporting 'pileup -g'.

The StatGen Library used 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 r983
   bgzf.c         - updated to the version from r983
   khash.h        - updated to the version from  r983
   knetfile.h     - has not changed between 0.1.7a and r983
   knetfile.c     - updated to the version from r983
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 used 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
