academic/samtools: Updated for version 1.10.

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>

5 files changed, 106 insertions, 39 deletions

diff --git a/academic/samtools/README b/academic/samtools/README
index ea600cbe2618..857bfbeaa753 100644
--- a/academic/samtools/README
+++ b/academic/samtools/README
@@ -1,11 +1,16 @@
-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
+SAM (Sequence Alignment/Map) format is a generic format for storing large 
+nucleotide sequence alignments. The original samtools package has been split 
+into three separate but tightly coordinated projects: htslib (C library for 
+handling high-throughput sequencing data), samtools (for handling SAM, BAM, 
+CRAM), and bcftools (for handling VCF and BCF).
 
-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.
+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. Note that the sam.h of htslib differs from sam.h coming 
+with samtools.
 
-Note that the sam.h of htslib differs from sam.h coming with samtools.
+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.
diff --git a/academic/samtools/README.references b/academic/samtools/README.references
new file mode 100644
index 000000000000..1d021bdd965b
--- /dev/null
+++ b/academic/samtools/README.references
@@ -0,0 +1,64 @@
+References:
+
+======================
+File formats
+
+
+The introduction of the SAM/BAM format and the samtools command line tool:
+
+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, The Sequence alignment/map (SAM) format and SAMtools, Bioinformatics (2009) 25(16) 2078-9 [19505943]
+
+
+Extension of the SAM/BAM format to support de novo assemblies:
+
+Cock PJA, Bonfield JK, Chevreux B, Li H, SAM/BAM format v1.5 extensions for de novo assemblies, bioRxiv (2015) 020024 [doi:10.1101/020024]
+
+
+The introduction of the CRAM format:
+
+Hsi-Yang Fritz M, Leinonen R, Cochrane G, and Birney E, Efficient storage of high throughput DNA sequencing data using reference-based compression, Genome Research (2011) 21(5) 734-740.
+The introduction of the VCF format:
+
+Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group, The variant call format and VCFtools, Bioinformatics (2011) 27(15) 2156-8
+
+======================
+Calling and analysis
+
+
+The original mpileup calling algorithm plus mathematical notes (mpileup/bcftools call -c):
+
+Li H, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics (2011) 27(21) 2987-93.
+Li H, Mathematical Notes on SAMtools Algorithms (2010)
+
+
+Mathematical notes for the updated multiallelic calling model (mpileup/bcftools call -m):
+
+Danecek P, Schiffels S, and Durbin R, Multiallelic calling model in bcftools (-m) (2014)
+
+
+Hidden Markov model for detecting runs of homozygosity (bcftools roh):
+
+Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, and Durbin R, BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data, Bioinformatics (2016) 32(11) 1749-51 
+
+
+Copy number variation/aneuploidy calling from microarray data (bcftools cnv/bcftools polysomy):
+
+Danecek P, McCarthy SA, HipSci Consortium, and Durbin R, A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data, PLoS One (2016) 11(5) e0155014 
+
+
+Haplotype-aware calling of variant consequences (bcftools csq):
+
+Danecek P, McCarthy SA, BCFtools/csq: Haplotype-aware variant consequences, Bioinformatics (2017) 33(13) 2037-39 
+
+======================
+Other
+
+
+Base alignment quality (BAQ) method improve SNP calling around INDELs:
+
+Li H, Improving SNP discovery by base alignment quality, Bioinformatics (2011) 27(8) 1157-8
+
+
+Segregation based QC metric originally implemented in SGA:
+
+Durbin R, Segregation based metric for variant call QC (2014)
diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild
index daa7e87dafc0..4a7efb30d8a2 100644
--- a/academic/samtools/samtools.SlackBuild
+++ b/academic/samtools/samtools.SlackBuild
@@ -3,7 +3,7 @@
 # Slackware build script for samtools
 
 # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com
-# Copyright 2017-2018 Rob van Nues # All rights reserved.
+# Copyright 2017-2020 Rob van Nues # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
 # permitted provided that the following conditions are met:
@@ -22,13 +22,13 @@
 #  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-PRGNAM=samtools
-VERSION=${VERSION:-1.9}
+PRGNAM=samtools			
+VERSION=${VERSION:-1.10}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
-# Some applications still rely on the legacy samtools API instead of using htslib
-# exclusively, in that case, install the headers in /usr/include/bam and the static
+# Some applications still rely on the legacy samtools API instead of using htslib 
+# exclusively, in that case, install the headers in /usr/include/bam and the static 
 # libbam library as well by declaring (uncommenting):
 #SAMLIB="yes"
 # and commenting out:
@@ -96,6 +96,17 @@ CXXFLAGS="$SLKCFLAGS" \
 make
 make install DESTDIR=$PKG
 
+mkdir -p $PKG/usr/share/$PRGNAM-$VERSION
+cp -a misc/*.lua $PKG/usr/share/$PRGNAM-$VERSION
+
+# include samtools-API if set above
+if [ "$SAMLIB" = "yes" ] ; then
+  mkdir -p $PKG/usr/include/bam
+  mkdir -p $PKG/usr/lib${LIBDIRSUFFIX}
+  install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}"
+  install -m644 *.h "$PKG/usr/include/bam"
+fi
+
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
   | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
 
@@ -106,24 +117,11 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
   AUTHORS LICENSE README INSTALL NEWS examples \
   $PKG/usr/doc/$PRGNAM-$VERSION
+cp $CWD/README.references $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 
-mkdir -p $PKG/usr/share/$PRGNAM-$VERSION
-
-cp -a \
-  misc/*.lua \
-  $PKG/usr/share/$PRGNAM-$VERSION
-
 mkdir -p $PKG/install
 cat $CWD/slack-desc > $PKG/install/slack-desc
 
-# include samtools-API if set above
-if [ "$SAMLIB" = "yes" ] ; then
-  mkdir -p $PKG/usr/include/bam
-  mkdir -p $PKG/usr/lib${LIBDIRSUFFIX}
-  install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}"
-  install -m644 *.h "$PKG/usr/include/bam"
-fi
-
 cd $PKG
 /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/samtools/samtools.info b/academic/samtools/samtools.info
index 1d724a44e4f2..05fe9a33a040 100644
--- a/academic/samtools/samtools.info
+++ b/academic/samtools/samtools.info
@@ -1,8 +1,8 @@
 PRGNAM="samtools"
-VERSION="1.9"
+VERSION="1.10"
 HOMEPAGE="http://www.htslib.org"
-DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2"
-MD5SUM="cca9a40d9b91b007af2ff905cb8b5924"
+DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2"
+MD5SUM="506b0b9b2628e1f3bbedd77855b4c709"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="htslib"
diff --git a/academic/samtools/slack-desc b/academic/samtools/slack-desc
index 8f1c434e47e5..e2e844e35711 100644
--- a/academic/samtools/slack-desc
+++ b/academic/samtools/slack-desc
@@ -8,12 +8,12 @@
         |-----handy-ruler------------------------------------------------------|
 samtools: samtools (Sequence Alignment/Map Tools)
 samtools:
-samtools: SAM (Sequence Alignment/Map) format is a generic format for
-samtools: storing large nucleotide sequence alignments. The original samtools 
-samtools: package has been split into three separate but tightly coordinated 
-samtools: projects: htslib (C-library for handling high-throughput sequencing 
-samtools: data); samtools (for handling SAM, BAM, CRAM) and bcftools (for 
-samtools: handling VCF, BCF). Both samtools and bcftools are set up to use
-samtools: system-wide installed hstlib sources.
-samtools: Home: http://www.htslib.org
+samtools: SAM (Sequence Alignment/Map) format is a generic format for storing
+samtools: large nucleotide sequence alignments. The original samtools package
+samtools: has been split into three separate but tightly coordinated projects:
+samtools: htslib (C-library for handling high-throughput sequencing data),
+samtools: samtools (for handling SAM, BAM, CRAM), and bcftools (for handling
+samtools: VCF and BCF).
+samtools:
+samtools: Homepage: http://www.htslib.org
 samtools: