biolibc: Update to 0.2.2.19

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Apr 24 10:28:29 2022 -0500
Changeset:	39ca33f97487f600edaa936e435892f2b3e346e4

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

Log Message:
biolibc: Update to 0.2.2.19

Use tsv_read_field_malloc() to declunkify VCF API
Add bl_vcf_skip_header(): bl_vcf_skip_meta_data() + header line
sam.c: Fix check for NULL qual field from tsv_skip_field()

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=39ca33f97487f600edaa936e435892f2b3e346e4

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         | 31 +++++++++++++++++++++++++------
 biolibc/buildlink3.mk |  2 +-
 biolibc/distinfo      |  6 +++---
 4 files changed, 31 insertions(+), 12 deletions(-)

diffs:
diff --git a/biolibc/Makefile b/biolibc/Makefile
index f6f935d2ed..b5c06e7df0 100644
--- a/biolibc/Makefile
+++ b/biolibc/Makefile
@@ -1,9 +1,9 @@
 # $NetBSD$
 
-DISTNAME=	biolibc-0.2.2.18
+DISTNAME=	biolibc-0.2.2.19
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG=	63e833a0f1e387143fca76491af58c2efd384501
+GITHUB_TAG=	00f7a94e21e6a520121d4f35072df0299b7667eb
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/auerlab/biolibc
diff --git a/biolibc/PLIST b/biolibc/PLIST
index dc672737b9..610927552e 100644
--- a/biolibc/PLIST
+++ b/biolibc/PLIST
@@ -195,16 +195,22 @@ man/man3/BL_VCF_FILTER.3
 man/man3/BL_VCF_FILTER_AE.3
 man/man3/BL_VCF_FORMAT.3
 man/man3/BL_VCF_FORMAT_AE.3
+man/man3/BL_VCF_FORMAT_ARRAY_SIZE.3
 man/man3/BL_VCF_FORMAT_LEN.3
-man/man3/BL_VCF_FORMAT_MAX.3
 man/man3/BL_VCF_ID.3
 man/man3/BL_VCF_ID_AE.3
 man/man3/BL_VCF_INFO.3
 man/man3/BL_VCF_INFO_AE.3
+man/man3/BL_VCF_INFO_ARRAY_SIZE.3
 man/man3/BL_VCF_INFO_LEN.3
-man/man3/BL_VCF_INFO_MAX.3
 man/man3/BL_VCF_MULTI_SAMPLES.3
 man/man3/BL_VCF_MULTI_SAMPLES_AE.3
+man/man3/BL_VCF_MULTI_SAMPLE_ARRAY_SIZES.3
+man/man3/BL_VCF_MULTI_SAMPLE_ARRAY_SIZES_AE.3
+man/man3/BL_VCF_MULTI_SAMPLE_COUNT.3
+man/man3/BL_VCF_MULTI_SAMPLE_LENS.3
+man/man3/BL_VCF_MULTI_SAMPLE_LENS_AE.3
+man/man3/BL_VCF_MULTI_SAMPLE_POINTER_ARRAY_SIZE.3
 man/man3/BL_VCF_OTHER_COUNT.3
 man/man3/BL_VCF_PHREDS.3
 man/man3/BL_VCF_PHREDS_AE.3
@@ -216,9 +222,13 @@ man/man3/BL_VCF_QUAL_AE.3
 man/man3/BL_VCF_REF.3
 man/man3/BL_VCF_REF_AE.3
 man/man3/BL_VCF_REF_COUNT.3
+man/man3/BL_VCF_SAMPLE_ARRAY_SIZE.3
+man/man3/BL_VCF_SAMPLE_LEN.3
 man/man3/BL_VCF_SAMPLE_MAX.3
 man/man3/BL_VCF_SINGLE_SAMPLE.3
 man/man3/BL_VCF_SINGLE_SAMPLE_AE.3
+man/man3/BL_VCF_SINGLE_SAMPLE_ARRAY_SIZE.3
+man/man3/BL_VCF_SINGLE_SAMPLE_LEN.3
 man/man3/biolibc.3
 man/man3/bl_align_map_seq_exact.3
 man/man3/bl_align_map_seq_sub.3
@@ -449,7 +459,6 @@ man/man3/bl_vcf_init.3
 man/man3/bl_vcf_parse_field_spec.3
 man/man3/bl_vcf_read_ss_call.3
 man/man3/bl_vcf_read_static_fields.3
-man/man3/bl_vcf_sample_alloc.3
 man/man3/bl_vcf_set_alt_ae.3
 man/man3/bl_vcf_set_alt_count.3
 man/man3/bl_vcf_set_alt_cpy.3
@@ -459,16 +468,24 @@ man/man3/bl_vcf_set_filter_ae.3
 man/man3/bl_vcf_set_filter_cpy.3
 man/man3/bl_vcf_set_format.3
 man/man3/bl_vcf_set_format_ae.3
+man/man3/bl_vcf_set_format_array_size.3
 man/man3/bl_vcf_set_format_cpy.3
 man/man3/bl_vcf_set_format_len.3
-man/man3/bl_vcf_set_format_max.3
 man/man3/bl_vcf_set_id_ae.3
 man/man3/bl_vcf_set_id_cpy.3
 man/man3/bl_vcf_set_info.3
 man/man3/bl_vcf_set_info_ae.3
+man/man3/bl_vcf_set_info_array_size.3
 man/man3/bl_vcf_set_info_cpy.3
 man/man3/bl_vcf_set_info_len.3
-man/man3/bl_vcf_set_info_max.3
+man/man3/bl_vcf_set_multi_sample_array_sizes.3
+man/man3/bl_vcf_set_multi_sample_array_sizes_ae.3
+man/man3/bl_vcf_set_multi_sample_array_sizes_cpy.3
+man/man3/bl_vcf_set_multi_sample_count.3
+man/man3/bl_vcf_set_multi_sample_lens.3
+man/man3/bl_vcf_set_multi_sample_lens_ae.3
+man/man3/bl_vcf_set_multi_sample_lens_cpy.3
+man/man3/bl_vcf_set_multi_sample_pointer_array_size.3
 man/man3/bl_vcf_set_multi_samples.3
 man/man3/bl_vcf_set_multi_samples_ae.3
 man/man3/bl_vcf_set_multi_samples_cpy.3
@@ -484,10 +501,12 @@ man/man3/bl_vcf_set_qual_cpy.3
 man/man3/bl_vcf_set_ref_ae.3
 man/man3/bl_vcf_set_ref_count.3
 man/man3/bl_vcf_set_ref_cpy.3
-man/man3/bl_vcf_set_sample_max.3
 man/man3/bl_vcf_set_single_sample.3
 man/man3/bl_vcf_set_single_sample_ae.3
+man/man3/bl_vcf_set_single_sample_array_size.3
 man/man3/bl_vcf_set_single_sample_cpy.3
+man/man3/bl_vcf_set_single_sample_len.3
+man/man3/bl_vcf_skip_header.3
 man/man3/bl_vcf_skip_meta_data.3
 man/man3/bl_vcf_write_ss_call.3
 man/man3/bl_vcf_write_static_fields.3
diff --git a/biolibc/buildlink3.mk b/biolibc/buildlink3.mk
index e25e3a840a..bf70406f14 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>=0.2.2.18
+BUILDLINK_API_DEPENDS.biolibc+=	biolibc>=0.2.2.19
 BUILDLINK_PKGSRCDIR.biolibc?=	../../wip/biolibc
 
 .include "../../wip/libxtend/buildlink3.mk"
diff --git a/biolibc/distinfo b/biolibc/distinfo
index 563b9e35c1..4ad052343a 100644
--- a/biolibc/distinfo
+++ b/biolibc/distinfo
@@ -1,5 +1,5 @@
 $NetBSD$
 
-BLAKE2s (biolibc-0.2.2.18-63e833a0f1e387143fca76491af58c2efd384501.tar.gz) = 6b85a0c3927d3a29e8d3af49c268962008e7fbdca17eae3facdd65c502bbd58a
-SHA512 (biolibc-0.2.2.18-63e833a0f1e387143fca76491af58c2efd384501.tar.gz) = 6016307f89f6deac90132af4b9fd6af3b16c14a20104df61f3e8ebf7aae92145490b4aa43d85434e82167ce6d2e4257124a92a41cef4f6ca5e29f9fbb5f7df53
-Size (biolibc-0.2.2.18-63e833a0f1e387143fca76491af58c2efd384501.tar.gz) = 135801 bytes
+BLAKE2s (biolibc-0.2.2.19-00f7a94e21e6a520121d4f35072df0299b7667eb.tar.gz) = cf425917a312cf02cf8acf026715d68d0454f2f4f6fe1ccaf7bc8f02b8cdcd85
+SHA512 (biolibc-0.2.2.19-00f7a94e21e6a520121d4f35072df0299b7667eb.tar.gz) = 037c6fd4e750a6f12425c594c05a4ca7d1a0dbaa2b5116f06224b4d33c819d046e0a8d6cc1312f36b16cb55ac926d8ac28954cb989c49a6f44f92c6edc47064c
+Size (biolibc-0.2.2.19-00f7a94e21e6a520121d4f35072df0299b7667eb.tar.gz) = 138310 bytes