biolibc: Update to 0.2.1.23

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Jan 24 09:02:16 2022 -0600
Changeset:	1707a903b3f214494779be87668535a5dfd4d475

Modified Files:
	biolibc/Makefile
	biolibc/PLIST
	biolibc/buildlink3.mk
	biolibc/distinfo

Log Message:
biolibc: Update to 0.2.1.23

Frame out a basic alignment class with a structure for alignment parameters
to accommodate different algorithms via a common API
Generalize the adapter matching functions to a new generic alignment API

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1707a903b3f214494779be87668535a5dfd4d475

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

diffstat:
 biolibc/Makefile      |  4 ++--
 biolibc/PLIST         | 12 ++++++++++--
 biolibc/buildlink3.mk |  2 +-
 biolibc/distinfo      |  6 +++---
 4 files changed, 16 insertions(+), 8 deletions(-)

diffs:
diff --git a/biolibc/Makefile b/biolibc/Makefile
index 959dd53446..673ab15360 100644
--- a/biolibc/Makefile
+++ b/biolibc/Makefile
@@ -1,9 +1,9 @@
 # $NetBSD$
 
-DISTNAME=	biolibc-0.2.1.14
+DISTNAME=	biolibc-0.2.1.23
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG=	b703ddcea5ddc43375cee1b08b31ab96ccfdcd5f
+GITHUB_TAG=	a446e51faef03f7ffcd7e8921adc9544ebff34f5
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/auerlab/biolibc
diff --git a/biolibc/PLIST b/biolibc/PLIST
index eee5319720..b1ae093a94 100644
--- a/biolibc/PLIST
+++ b/biolibc/PLIST
@@ -1,4 +1,8 @@
 @comment $NetBSD$
+include/biolibc/align-accessors.h
+include/biolibc/align-mutators.h
+include/biolibc/align-rvs.h
+include/biolibc/align.h
 include/biolibc/bed-accessors.h
 include/biolibc/bed-mutators.h
 include/biolibc/bed-rvs.h
@@ -46,6 +50,8 @@ lib/libbiolibc.a
 lib/libbiolibc.so
 lib/libbiolibc.so.2
 lib/libbiolibc.so.2.0
+man/man3/BL_ALIGN_MAX_MISMATCH_PERCENT.3
+man/man3/BL_ALIGN_MIN_MATCH.3
 man/man3/BL_BED_BLOCK_COUNT.3
 man/man3/BL_BED_BLOCK_SIZES.3
 man/man3/BL_BED_BLOCK_SIZES_AE.3
@@ -197,6 +203,10 @@ man/man3/BL_VCF_SAMPLE_MAX.3
 man/man3/BL_VCF_SINGLE_SAMPLE.3
 man/man3/BL_VCF_SINGLE_SAMPLE_AE.3
 man/man3/biolibc.3
+man/man3/bl_align_map_seq_exact.3
+man/man3/bl_align_map_seq_sub.3
+man/man3/bl_align_set_max_mismatch_percent.3
+man/man3/bl_align_set_min_match.3
 man/man3/bl_bed_check_order.3
 man/man3/bl_bed_gff_cmp.3
 man/man3/bl_bed_read.3
@@ -239,8 +249,6 @@ man/man3/bl_fasta_set_seq_len.3
 man/man3/bl_fasta_write.3
 man/man3/bl_fastq_3p_trim.3
 man/man3/bl_fastq_find_3p_low_qual.3
-man/man3/bl_fastq_find_adapter_exact.3
-man/man3/bl_fastq_find_adapter_smart.3
 man/man3/bl_fastq_free.3
 man/man3/bl_fastq_init.3
 man/man3/bl_fastq_name_cmp.3
diff --git a/biolibc/buildlink3.mk b/biolibc/buildlink3.mk
index 211abe9f5f..8407e301ed 100644
--- a/biolibc/buildlink3.mk
+++ b/biolibc/buildlink3.mk
@@ -5,7 +5,7 @@ BUILDLINK_TREE+=	biolibc
 .if !defined(BIOLIBC_BUILDLINK3_MK)
 BIOLIBC_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.biolibc+=	biolibc>=0.2.1.14
+BUILDLINK_API_DEPENDS.biolibc+=	biolibc>=0.2.1.23
 BUILDLINK_PKGSRCDIR.biolibc?=	../../wip/biolibc
 
 .include "../../wip/libxtend/buildlink3.mk"
diff --git a/biolibc/distinfo b/biolibc/distinfo
index c5f8f246b7..9ff7e4b68b 100644
--- a/biolibc/distinfo
+++ b/biolibc/distinfo
@@ -1,5 +1,5 @@
 $NetBSD$
 
-BLAKE2s (biolibc-0.2.1.14-b703ddcea5ddc43375cee1b08b31ab96ccfdcd5f.tar.gz) = b33c7de5ad072cb5374ed066e6d5ca0cd7df56d65db30cf27b00488759af7d95
-SHA512 (biolibc-0.2.1.14-b703ddcea5ddc43375cee1b08b31ab96ccfdcd5f.tar.gz) = ffef192b9e8b0f31c212282310f8a5dee83e48d2708ac037eb6585dc527ca37aa7d6801b5707532adbf42fe6b80ad30f0d427bb75b232359c33acb0336617c65
-Size (biolibc-0.2.1.14-b703ddcea5ddc43375cee1b08b31ab96ccfdcd5f.tar.gz) = 117812 bytes
+BLAKE2s (biolibc-0.2.1.23-a446e51faef03f7ffcd7e8921adc9544ebff34f5.tar.gz) = d6369a8d386813271de2e3e055821e9edb7e770a69f807fa0b8bcd2dfaeac529
+SHA512 (biolibc-0.2.1.23-a446e51faef03f7ffcd7e8921adc9544ebff34f5.tar.gz) = 6b47a7d405f85a89233d53cd534e69b3ccec301eed44dbf28b958e2edda90d617031a95c5045a33054decb8770447e77a4e9c93353715b4963b807c49eb55a15
+Size (biolibc-0.2.1.23-a446e51faef03f7ffcd7e8921adc9544ebff34f5.tar.gz) = 120071 bytes