Remove razip source code and remaining vestiges

Samtools no longer uses razip or RAZF files itself.  The code remains
available in older releases and on the `standalone` branch.

.gitignore

@@ -12,7 +12,6 @@ lib*.a
 /misc/md5fa
 /misc/md5sum-lite
 /misc/wgsim
-/razip
 /samtools
 
 /TAGS

AUTHORS

@@ -7,14 +7,12 @@ underlying indexable compression format for the BAM format. BGZF does
 not support arithmetic between file offsets.
 
 Jue Ruan for the Beijing Genome Institute designed and implemented the
-RAZF format, an alternative indexable compression format. RAZF supports
-arithmetic between file offsets, at the cost of increased index file
-size and the full compatibility with gzip. RAZF is optional and only
-used in `faidx' for indexing RAZF compressed fasta files.
+RAZF format, an alternative indexable compression format. RAZF is no longer
+used by or provided with SAMtools. Source code remains available in older
+SAMtools 0.1.x releases and from the standalone branch in the repository.
 
 Colin Hercus updated novo2sam.pl to support gapped alignment by
 novoalign.
 
 Petr Danecek contributed the header parsing library sam_header.c and 
-sam2vcf.pl script and added knet support to the RAZF library.
-
+sam2vcf.pl script.

INSTALL

@@ -2,9 +2,10 @@ System Requirements
 ===================
 
 SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
-preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
-file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
-diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.
+preferred.
+
+SAMtools' faidx is able to index a bgzip-compressed FASTA file to save
+diskspace.
 
 The text-based viewer (tview) requires the GNU ncurses library
 <http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
@@ -20,8 +21,7 @@ as -lnurses. This can be set in Makefile by setting LIBCURSES= -lcurses vs
 Compilation
 ===========
 
-Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
-razip with `make razip'.
+Type `make' to compile samtools.
 
 
 Installation

samtools.1

@@ -270,7 +270,7 @@ specificity a little bit.
 The
 .BR faidx -indexed
 reference file in the FASTA format. The file can be optionally compressed by
-.BR razip .
+.BR bgzip .
 [null]
 .TP
 .BI -l \ FILE
@@ -483,7 +483,7 @@ will index the file and create
 on the disk. If regions are specified, the subsequences will be
 retrieved and printed to stdout in the FASTA format. The input file can
 be compressed in the
-.B RAZF
+.B BGZF
 format.
 
 .TP
@@ -828,8 +828,7 @@ although a little slower.
 .SH AUTHOR
 .PP
 Heng Li from the Sanger Institute wrote the C version of samtools. Bob
-Handsaker from the Broad Institute implemented the BGZF library and Jue
-Ruan from Beijing Genomics Institute wrote the RAZF library. John
+Handsaker from the Broad Institute implemented the BGZF library. John
 Marshall and Petr Danecek contribute to the source code and various
 people from the 1000 Genomes Project have contributed to the SAM format
 specification.