samtools: updated to 1.9

Release 1.9:

 * Samtools mpileup VCF and BCF output is now deprecated.  It is still
   functional, but will warn.  Please use bcftools mpileup instead.

 * Samtools mpileup now handles the '-d' max_depth option differently.  There
   is no longer an enforced minimum, and '-d 0' is interpreted as limitless
   (no maximum - warning this may be slow).  The default per-file depth is
   now 8000, which matches the value mpileup used to use when processing
   a single sample.  To get the previous default behaviour use the higher
   of 8000 divided by the number of samples across all input files, or 250.

 * Samtools stats new features:

   - The '--remove-overlaps' option discounts overlapping portions of
     templates when computing coverage and mapped base counting.

   - When a target file is in use, the number of bases inside the
     target is printed and the percentage of target bases with coverage
     above a given threshold specified by the '--cov-threshold' option.

   - Split base composition and length statistics by first and last reads.

 * Samtools faidx new features:

   - Now takes long options.

   - Now warns about zero-length and truncated sequences due to the
     requested range being beyond the end of the sequence.

   - Gets a new option (--continue) that allows it to carry on
     when a requested sequence was not in the index.

   - It is now possible to supply the list of regions to output in a text
     file using the new '--region-file' option.

   - New '-i' option to make faidx return the reverse complement of
     the regions requested.

   - faidx now works on FASTQ (returning FASTA) and added a new
     fqidx command to index and return FASTQ.

 * Samtools collate now has a fast option '-f' that only operates on
   primary pairs, dropping secondary and supplementary.  It tries to write
   pairs to the final output file as soon as both reads have been found.

 * Samtools bedcov gets a new '-j' option to make it ignore deletions (D) and
   reference skips (N) when computing coverage.

 * Small speed up to samtools coordinate sort, by converting it to use
   radix sort.

 * Samtools idxstats now works on SAM and CRAM files, however this
   isn't fast due to some information lacking from indices.

 * Compression levels may now be specified with the level=N
   output-fmt-option.  E.g. with -O bam,level=3.

 * Various documentation improvements.

 * Bug-fixes:

   - Improved error reporting in several places.

   - Various test improvements.

   - Fixed failures in the multi-region iterator (view -M) when regions
     provided via BED files include overlaps

   - Samtools stats now counts '=' and 'X' CIGAR operators when
     counting mapped bases.

   - Samtools stats has fixes for insert size filtering (-m, -i).

   - Samtools stats -F now longer negates an earlier -d option.

   - Fix samtools stats crash when using a target region.

   - Samtools sort now keeps to a single thread when the -@ option is absent.
     Previously it would spawn a writer thread, which could cause the CPU
     usage to go slightly over 100%.

   - Fixed samtools phase '-A' option which was incorrectly defined to take
     a parameter.

   - Fixed compilation problems when using C_INCLUDE_PATH.

   - Fixed --version when built from a Git repository.

   - Use noenhanced mode for title in plot-bamstats.  Prevents unwanted
     interpretation of characters like underscore in gnuplot version 5.

   - blast2sam.pl now reports perfect match hits (no indels or mismatches).

   - Fixed bug in fasta and fastq subcommands where stdout would not be flushed
     correctly if the -0 option was used.

   - Fixed invalid memory access in mpileup and depth on alignment records
     where the sequence is absent.

2 files changed, 19 insertions, 18 deletions

diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index acb712e98a9..c4018af7e21 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -1,26 +1,27 @@
-# $NetBSD: Makefile,v 1.2 2018/08/22 09:42:59 wiz Exp $
+# $NetBSD: Makefile,v 1.3 2018/11/06 10:49:41 adam Exp $
 
-DISTNAME=	samtools-1.8
-PKGREVISION=	1
+DISTNAME=	samtools-1.9
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
-GITHUB_TAG=	${PKGVERSION_NOREV}
+EXTRACT_SUFX=	.tar.bz2
+GITHUB_RELEASE=	${PKGVERSION_NOREV}
 
 MAINTAINER=	bacon@NetBSD.org
 HOMEPAGE=	http://www.htslib.org/
 COMMENT=	Tools for manipulating next-generation sequencing data
 LICENSE=	mit
 
-USE_TOOLS+=	autoconf automake autoreconf gmake perl:run
-GNU_CONFIGURE=	yes
-REPLACE_PERL=	misc/*.pl misc/plot-bamstats test/test.pl
-REPLACE_PYTHON=	misc/*.py
+USE_TOOLS+=		gmake perl:run
+GNU_CONFIGURE=		yes
+CONFIGURE_ARGS+=	--with-htslib=system
+TEST_TARGET=		test
 
-pre-configure:
-	cd ${WRKSRC} && autoreconf
+REPLACE_PERL=		misc/*.pl
+REPLACE_PERL+=		misc/plot-bamstats
+REPLACE_PERL+=		test/test.pl
+REPLACE_PYTHON=		misc/*.py
 
-.include "../../mk/curses.buildlink3.mk"
-.include "../../lang/python/application.mk"
 .include "../../biology/htslib/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/curses.buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index 59523c11fb1..5100c09cb1f 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2018/05/07 18:37:31 bacon Exp $
+$NetBSD: distinfo,v 1.2 2018/11/06 10:49:41 adam Exp $
 
-SHA1 (samtools-1.8.tar.gz) = 5ac70ba4c324c223398ab4c0689933564985303c
-RMD160 (samtools-1.8.tar.gz) = 47e4fde82a686669322fd330374aa37b148b7954
-SHA512 (samtools-1.8.tar.gz) = 82e4d5f855f944cc989902154a99eada2b4c81939bd936fa1d471cf9ff01e03c8a7f773928ae55ef691f2827aa4076126678940bb89a322fa56d83c517677d0c
-Size (samtools-1.8.tar.gz) = 4047378 bytes
+SHA1 (samtools-1.9.tar.bz2) = 267191dc2f5d24eb0b22c0094138270ed5384241
+RMD160 (samtools-1.9.tar.bz2) = b7f49e1bdd569f63ec53330f43df7e5566ba8a16
+SHA512 (samtools-1.9.tar.bz2) = 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
+Size (samtools-1.9.tar.bz2) = 4440405 bytes