CVS commit: pkgsrc/biology/htslib

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Tue Dec 13 10:27:03 UTC 2022

Modified Files:
        pkgsrc/biology/htslib: Makefile distinfo

Log Message:
htslib: updated to 1.16

1.16

Make hfile_s3 refresh AWS credentials on expiry in order to make HTSlib work better with AWS IAM credentials, which have a limited lifespan.

Allow BAM headers between 2GB and 4GB in size once more. This is not permitted in the BAM specification but was allowed in an earlier version of HTSlib. There is now a warning at 2GB and a hard 
failure at 4GB.

Improve error message when failing to load an index.

Permit MM (base modification) tags containing . and ? suffixes. These define implicit vs explicit coordinates. See the SAM tags specification for details.

Warn if spaces instead of tabs are detected in a VCF file to prevent confusion.

Add an sclen filter expression keyword. This is the length of a soft-clip, both left and right end. It may be combined with qlen (qlen-sclen) to obtain the number of bases in the query sequence that 
have been aligned to the genome ie it provides a way to compare local-alignment vs global-alignment length.

Improve error messages for CRAM reference mismatches. If the user specifies the wrong reference, the CRAM slice header MD5sum checks fail. We now report the SQ line M5 string too so it is possible to 
validate against the whole chr in the ref.fa file. The error message has also been improved to report the reference name instead of #num. Finally, we now hint at the likely cause, which counters the 
misleading samtools supplied error of "truncated or corrupt" file.

Expose more of the CRAM API and add new functionality to extract the reference from a CRAM file.

Improvements to the implementation of embedded references in CRAM where no external reference is specified.

The CRAM writer now allows alignment records with RG:Z: aux tags that don't have a corresponding @RG ID in the file header. Previously these tags would have been silently dropped. HTSlib will 
complain whenever it has to add one though, as such tags do not conform to recommended practice for the SAM, BAM and CRAM formats.

Set tab delimiter in man page for tabix GFF3 sort.

When using libdeflate, the 1...9 scale of BGZF compression levels is now remapped to the 1...12 range used by libdeflate instead of being passed directly. In particular, HTSlib levels 8 and 9 now map 
to libdeflate levels 10 and 12, so it is possible to select the highest (but slowest) compression offered by libdeflate.

The VCF variant API has been extended so that it can return separate flags for INS and DEL variants as well as the existing INDEL one. These flags have not been added to the old 
bcf_get_variant_types() interface as it could break existing users. To access them, it is necessary to use new functions bcf_has_variant_type() and bcf_has_variant_types().

The missing, but trivial, le_to_u8() function has been added to hts_endian.

bcf_format_gt() now works properly on big-endian platforms.


To generate a diff of this commit:
cvs rdiff -u -r1.28 -r1.29 pkgsrc/biology/htslib/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/htslib/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/htslib/Makefile
diff -u pkgsrc/biology/htslib/Makefile:1.28 pkgsrc/biology/htslib/Makefile:1.29
--- pkgsrc/biology/htslib/Makefile:1.28 Wed Oct 26 10:31:14 2022
+++ pkgsrc/biology/htslib/Makefile      Tue Dec 13 10:27:03 2022
@@ -1,10 +1,9 @@
-# $NetBSD: Makefile,v 1.28 2022/10/26 10:31:14 wiz Exp $
+# $NetBSD: Makefile,v 1.29 2022/12/13 10:27:03 adam Exp $
 
-DISTNAME=      htslib-1.15.1
-PKGREVISION=   1
+DISTNAME=      htslib-1.16
 CATEGORIES=    biology
-# Github-generated distfiles are incomplete, use custom tarballs instead
-MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/htslib/releases/download/${PKGVERSION_NOREV}/}
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
+GITHUB_RELEASE=        ${PKGVERSION_NOREV}
 EXTRACT_SUFX=  .tar.bz2
 
 MAINTAINER=    bacon%NetBSD.org@localhost
@@ -14,6 +13,10 @@ LICENSE=     mit
 
 USE_TOOLS+=            autoconf automake autoreconf bash gmake perl
 GNU_CONFIGURE=         yes
+CONFIGURE_ARGS+=       --enable-libcurl
+PKGCONFIG_OVERRIDE=    htslib.pc.in
+TEST_TARGET=           test
+MAKE_ENV+=             BUILT_TEST_PROGRAMS=''
 
 SUBST_CLASSES+=                version
 SUBST_STAGE.version=   pre-configure
@@ -22,11 +25,6 @@ SUBST_FILES.version= configure.ac
 
 REPLACE_PERL+=         test/*.pl
 
-CONFIGURE_ARGS+=       --enable-libcurl
-PKGCONFIG_OVERRIDE=    htslib.pc.in
-TEST_TARGET=           test
-MAKE_ENV+=             BUILT_TEST_PROGRAMS=''
-
 pre-configure:
        cd ${WRKSRC} && autoreconf -if
 

Index: pkgsrc/biology/htslib/distinfo
diff -u pkgsrc/biology/htslib/distinfo:1.9 pkgsrc/biology/htslib/distinfo:1.10
--- pkgsrc/biology/htslib/distinfo:1.9  Tue Jul  5 11:00:16 2022
+++ pkgsrc/biology/htslib/distinfo      Tue Dec 13 10:27:03 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.9 2022/07/05 11:00:16 adam Exp $
+$NetBSD: distinfo,v 1.10 2022/12/13 10:27:03 adam Exp $
 
-BLAKE2s (htslib-1.15.1.tar.bz2) = 7d7498964c0bd934ba24450ebb86584f82606df788f3f126d76fd9e8fdd9d9b6
-SHA512 (htslib-1.15.1.tar.bz2) = 69d0c7f3ac50a9b9c579e9b3479b6745fc30d0ac838ff14695cf4e3da593854350e345ed1f4a496931ef57395f3416da4316903488f3e641f1e00fec544f3620
-Size (htslib-1.15.1.tar.bz2) = 4141140 bytes
+BLAKE2s (htslib-1.16.tar.bz2) = 5a4620982ac745706107fd0646de630b2410d133b4966fffa304ef62bb345beb
+SHA512 (htslib-1.16.tar.bz2) = 9fa0b1f9bba50f889d4542825c9543fb3b34c13b4cc0e18940a66fafd130749574bfa2c2663d8b39f0b4ed2b298bf130367cda1b17b2929093d64b386730cbc5
+Size (htslib-1.16.tar.bz2) = 4466776 bytes