[pkgsrc/trunk]: pkgsrc/biology/biolibc biology/biolibc: Update to 0.2.3

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/e611b4098b6c
branches:  trunk
changeset: 380660:e611b4098b6c
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Sat Jun 11 19:42:39 2022 +0000

description:
biology/biolibc: Update to 0.2.3

Expand use of tsv_read_field_malloc() to improve memory efficiency
Add SAM bit flag constants
Import SAM-GFF compare functions from diffanal
Updates for libxtend DSV API changes
Numerous minor bug fixes and enhancements
Changes: https://github.com/auerlab/biolibc/releases

diffstat:

 biology/biolibc/Makefile      |   4 +-
 biology/biolibc/PLIST         |  61 ++++++++++++++++++++++++++++++++++++++----
 biology/biolibc/buildlink3.mk |   4 +-
 biology/biolibc/distinfo      |   8 ++--
 4 files changed, 62 insertions(+), 15 deletions(-)

diffs (254 lines):

diff -r 8dbd2279a97c -r e611b4098b6c biology/biolibc/Makefile
--- a/biology/biolibc/Makefile  Sat Jun 11 19:39:40 2022 +0000
+++ b/biology/biolibc/Makefile  Sat Jun 11 19:42:39 2022 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.8 2022/03/15 21:06:32 bacon Exp $
+# $NetBSD: Makefile,v 1.9 2022/06/11 19:42:39 bacon Exp $
 
-DISTNAME=      biolibc-0.2.2
+DISTNAME=      biolibc-0.2.3
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
 
diff -r 8dbd2279a97c -r e611b4098b6c biology/biolibc/PLIST
--- a/biology/biolibc/PLIST     Sat Jun 11 19:39:40 2022 +0000
+++ b/biology/biolibc/PLIST     Sat Jun 11 19:42:39 2022 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.8 2022/03/15 21:06:32 bacon Exp $
+@comment $NetBSD: PLIST,v 1.9 2022/06/11 19:42:39 bacon Exp $
 include/biolibc/align-accessors.h
 include/biolibc/align-mutators.h
 include/biolibc/align-rvs.h
@@ -105,11 +105,15 @@
 man/man3/BL_FASTX_}.3
 man/man3/BL_GFF_ATTRIBUTES.3
 man/man3/BL_GFF_ATTRIBUTES_AE.3
+man/man3/BL_GFF_ATTRIBUTES_ARRAY_SIZE.3
+man/man3/BL_GFF_ATTRIBUTES_LEN.3
 man/man3/BL_GFF_END.3
 man/man3/BL_GFF_FEATURE_ID.3
 man/man3/BL_GFF_FEATURE_ID_AE.3
 man/man3/BL_GFF_FEATURE_NAME.3
 man/man3/BL_GFF_FEATURE_NAME_AE.3
+man/man3/BL_GFF_FEATURE_PARENT.3
+man/man3/BL_GFF_FEATURE_PARENT_AE.3
 man/man3/BL_GFF_FILE_POS.3
 man/man3/BL_GFF_INDEX_ARRAY_SIZE.3
 man/man3/BL_GFF_INDEX_COUNT.3
@@ -167,6 +171,8 @@
 man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3
 man/man3/BL_SAM_CIGAR.3
 man/man3/BL_SAM_CIGAR_AE.3
+man/man3/BL_SAM_CIGAR_ARRAY_SIZE.3
+man/man3/BL_SAM_CIGAR_LEN.3
 man/man3/BL_SAM_FLAG.3
 man/man3/BL_SAM_MAPQ.3
 man/man3/BL_SAM_PNEXT.3
@@ -175,6 +181,7 @@
 man/man3/BL_SAM_QNAME_AE.3
 man/man3/BL_SAM_QUAL.3
 man/man3/BL_SAM_QUAL_AE.3
+man/man3/BL_SAM_QUAL_ARRAY_SIZE.3
 man/man3/BL_SAM_QUAL_LEN.3
 man/man3/BL_SAM_RNAME.3
 man/man3/BL_SAM_RNAME_AE.3
@@ -182,6 +189,7 @@
 man/man3/BL_SAM_RNEXT_AE.3
 man/man3/BL_SAM_SEQ.3
 man/man3/BL_SAM_SEQ_AE.3
+man/man3/BL_SAM_SEQ_ARRAY_SIZE.3
 man/man3/BL_SAM_SEQ_LEN.3
 man/man3/BL_SAM_TLEN.3
 man/man3/BL_VCF_ALT.3
@@ -193,16 +201,22 @@
 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
@@ -214,9 +228,13 @@
 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
@@ -304,7 +322,9 @@
 man/man3/bl_fastx_set_fastq.3
 man/man3/bl_fastx_set_format.3
 man/man3/bl_fastx_write.3
+man/man3/bl_gff_copy.3
 man/man3/bl_gff_copy_header.3
+man/man3/bl_gff_dup.3
 man/man3/bl_gff_extract_attribute.3
 man/man3/bl_gff_free.3
 man/man3/bl_gff_index_add.3
@@ -325,9 +345,13 @@
 man/man3/bl_gff_index_set_start_cpy.3
 man/man3/bl_gff_init.3
 man/man3/bl_gff_read.3
+man/man3/bl_gff_sam_cmp.3
+man/man3/bl_gff_sam_overlap.3
 man/man3/bl_gff_set_attributes.3
 man/man3/bl_gff_set_attributes_ae.3
+man/man3/bl_gff_set_attributes_array_size.3
 man/man3/bl_gff_set_attributes_cpy.3
+man/man3/bl_gff_set_attributes_len.3
 man/man3/bl_gff_set_end.3
 man/man3/bl_gff_set_feature_id.3
 man/man3/bl_gff_set_feature_id_ae.3
@@ -335,6 +359,9 @@
 man/man3/bl_gff_set_feature_name.3
 man/man3/bl_gff_set_feature_name_ae.3
 man/man3/bl_gff_set_feature_name_cpy.3
+man/man3/bl_gff_set_feature_parent.3
+man/man3/bl_gff_set_feature_parent_ae.3
+man/man3/bl_gff_set_feature_parent_cpy.3
 man/man3/bl_gff_set_file_pos.3
 man/man3/bl_gff_set_gene_name_cpy.3
 man/man3/bl_gff_set_phase.3
@@ -400,11 +427,19 @@
 man/man3/bl_sam_buff_set_unmapped_alignments.3
 man/man3/bl_sam_buff_shift.3
 man/man3/bl_sam_copy.3
+man/man3/bl_sam_copy_header.3
+man/man3/bl_sam_fclose.3
+man/man3/bl_sam_fopen.3
 man/man3/bl_sam_free.3
+man/man3/bl_sam_gff_cmp.3
+man/man3/bl_sam_gff_overlap.3
 man/man3/bl_sam_init.3
 man/man3/bl_sam_read.3
+man/man3/bl_sam_set_cigar.3
 man/man3/bl_sam_set_cigar_ae.3
+man/man3/bl_sam_set_cigar_array_size.3
 man/man3/bl_sam_set_cigar_cpy.3
+man/man3/bl_sam_set_cigar_len.3
 man/man3/bl_sam_set_flag.3
 man/man3/bl_sam_set_mapq.3
 man/man3/bl_sam_set_pnext.3
@@ -413,6 +448,7 @@
 man/man3/bl_sam_set_qname_cpy.3
 man/man3/bl_sam_set_qual.3
 man/man3/bl_sam_set_qual_ae.3
+man/man3/bl_sam_set_qual_array_size.3
 man/man3/bl_sam_set_qual_cpy.3
 man/man3/bl_sam_set_qual_len.3
 man/man3/bl_sam_set_rname_ae.3
@@ -421,9 +457,11 @@
 man/man3/bl_sam_set_rnext_cpy.3
 man/man3/bl_sam_set_seq.3
 man/man3/bl_sam_set_seq_ae.3
+man/man3/bl_sam_set_seq_array_size.3
 man/man3/bl_sam_set_seq_cpy.3
 man/man3/bl_sam_set_seq_len.3
 man/man3/bl_sam_set_tlen.3
+man/man3/bl_sam_skip_header.3
 man/man3/bl_sam_write.3
 man/man3/bl_vcf_call_downstream_of_alignment.3
 man/man3/bl_vcf_call_in_alignment.3
@@ -434,7 +472,6 @@
 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
@@ -444,16 +481,24 @@
 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
@@ -469,10 +514,12 @@
 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 -r 8dbd2279a97c -r e611b4098b6c biology/biolibc/buildlink3.mk
--- a/biology/biolibc/buildlink3.mk     Sat Jun 11 19:39:40 2022 +0000
+++ b/biology/biolibc/buildlink3.mk     Sat Jun 11 19:42:39 2022 +0000
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.8 2022/03/15 21:06:32 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.9 2022/06/11 19:42:39 bacon Exp $
 
 BUILDLINK_TREE+=       biolibc
 
 .if !defined(BIOLIBC_BUILDLINK3_MK)
 BIOLIBC_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.2.2
+BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.2.3
 BUILDLINK_PKGSRCDIR.biolibc?=  ../../biology/biolibc
 
 .include "../../devel/libxtend/buildlink3.mk"
diff -r 8dbd2279a97c -r e611b4098b6c biology/biolibc/distinfo
--- a/biology/biolibc/distinfo  Sat Jun 11 19:39:40 2022 +0000
+++ b/biology/biolibc/distinfo  Sat Jun 11 19:42:39 2022 +0000
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.10 2022/03/15 21:06:32 bacon Exp $
+$NetBSD: distinfo,v 1.11 2022/06/11 19:42:39 bacon Exp $
 
-BLAKE2s (biolibc-0.2.2.tar.gz) = 41c301bb2c43693150b38629e5d8974589160334523783707f2daf3742dfc184
-SHA512 (biolibc-0.2.2.tar.gz) = c9ae6e36e344686856a77d961aed628ee8f4f99be5c6740d017bbb3378437fce41a063ca2d6370a4173acce2e7d3f45fa4563d7e52dd8bc024b86458244129d2
-Size (biolibc-0.2.2.tar.gz) = 129251 bytes
+BLAKE2s (biolibc-0.2.3.tar.gz) = cf90b6e8f11ccdac136ad4434b5e959f634d4423b4b037f351e8dd598241b288
+SHA512 (biolibc-0.2.3.tar.gz) = 53fa93189517d3632b5cacadeae1d61eef725b5381be15cadb4150e08dbd2bce9e5788cdc71f40bbd658b3c64ba7521436f7cad6676ce92dac735e769f92f24d
+Size (biolibc-0.2.3.tar.gz) = 140008 bytes