academic/samtools: Updated for version 1.9 + new maintainer.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 9 insertions, 20 deletions

diff --git a/academic/samtools/README b/academic/samtools/README
index 0203586f94..ea600cbe26 100644
--- a/academic/samtools/README
+++ b/academic/samtools/README
@@ -1,22 +1,11 @@
-SAM (Sequence Alignment/Map) format is a generic format for storing
-large nucleotide sequence alignments. SAM aims to be a format that:
+Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed
+in a single samtools-0.1.x package.
+This old version remains available from SBo as samtools-legacy
 
-- Is flexible enough to store all the alignment information generated
-  by various alignment programs
-- Is simple enough to be easily generated by alignment programs or
-  converted from existing alignment formats
-- Is compact in file size
-- Allows most of operations on the alignment to work on a stream
-  without loading the whole alignment into memory
-- Allows the file to be indexed by genomic position to efficiently
-  retrieve all reads aligning to a locus. 
+Samtools is now distributed as an individual package.
+Installation is set up so that the code uses an external HTSlib (also at SBo).
+Although deprecated upstream, in the case that people need parts of samtools-legacy
+(e.g header files or libbam) these can be installed from this package by modifying
+the samtools.Slackbuild.
 
-SAM Tools provide various utilities for manipulating alignments in the
-SAM format, including sorting, merging, indexing and generating 
-alignments in a per-position format.
-
-Publication:
-Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N.,
-Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data
-Processing Subgroup (2009) The Sequence alignment/map (SAM) format and
-SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
+Note that the sam.h of htslib differs from sam.h coming with samtools.