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/tags

3 files changed, 57 insertions, 10 deletions

diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile
index 465f7ea9a665..f828f7e98752 100644
--- a/biology/biolibc/Makefile
+++ b/biology/biolibc/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	biolibc
-DISTVERSION=	0.2.2
+DISTVERSION=	0.2.3
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo
index c319bf83d1ed..32220523e8e5 100644
--- a/biology/biolibc/distinfo
+++ b/biology/biolibc/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1647347323
-SHA256 (auerlab-biolibc-0.2.2_GH0.tar.gz) = b2d8ef23ce93321cc624fb1c7851e1353b12ac89ec0bac6a4f9ae0f3648869e4
-SIZE (auerlab-biolibc-0.2.2_GH0.tar.gz) = 129251
+TIMESTAMP = 1654950759
+SHA256 (auerlab-biolibc-0.2.3_GH0.tar.gz) = f3c99684a1b8a54497b190e9057e509d9a669295300025ead2ef29aa148ad750
+SIZE (auerlab-biolibc-0.2.3_GH0.tar.gz) = 140008
diff --git a/biology/biolibc/pkg-plist b/biology/biolibc/pkg-plist
index c0167ab0df06..dfbe6a49d997 100644
--- a/biology/biolibc/pkg-plist
+++ b/biology/biolibc/pkg-plist
@@ -104,11 +104,15 @@ man/man3/BL_FASTX_UNION.3.gz
 man/man3/BL_FASTX_}.3.gz
 man/man3/BL_GFF_ATTRIBUTES.3.gz
 man/man3/BL_GFF_ATTRIBUTES_AE.3.gz
+man/man3/BL_GFF_ATTRIBUTES_ARRAY_SIZE.3.gz
+man/man3/BL_GFF_ATTRIBUTES_LEN.3.gz
 man/man3/BL_GFF_END.3.gz
 man/man3/BL_GFF_FEATURE_ID.3.gz
 man/man3/BL_GFF_FEATURE_ID_AE.3.gz
 man/man3/BL_GFF_FEATURE_NAME.3.gz
 man/man3/BL_GFF_FEATURE_NAME_AE.3.gz
+man/man3/BL_GFF_FEATURE_PARENT.3.gz
+man/man3/BL_GFF_FEATURE_PARENT_AE.3.gz
 man/man3/BL_GFF_FILE_POS.3.gz
 man/man3/BL_GFF_INDEX_ARRAY_SIZE.3.gz
 man/man3/BL_GFF_INDEX_COUNT.3.gz
@@ -166,6 +170,8 @@ man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3.gz
 man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3.gz
 man/man3/BL_SAM_CIGAR.3.gz
 man/man3/BL_SAM_CIGAR_AE.3.gz
+man/man3/BL_SAM_CIGAR_ARRAY_SIZE.3.gz
+man/man3/BL_SAM_CIGAR_LEN.3.gz
 man/man3/BL_SAM_FLAG.3.gz
 man/man3/BL_SAM_MAPQ.3.gz
 man/man3/BL_SAM_PNEXT.3.gz
@@ -174,6 +180,7 @@ man/man3/BL_SAM_QNAME.3.gz
 man/man3/BL_SAM_QNAME_AE.3.gz
 man/man3/BL_SAM_QUAL.3.gz
 man/man3/BL_SAM_QUAL_AE.3.gz
+man/man3/BL_SAM_QUAL_ARRAY_SIZE.3.gz
 man/man3/BL_SAM_QUAL_LEN.3.gz
 man/man3/BL_SAM_RNAME.3.gz
 man/man3/BL_SAM_RNAME_AE.3.gz
@@ -181,6 +188,7 @@ man/man3/BL_SAM_RNEXT.3.gz
 man/man3/BL_SAM_RNEXT_AE.3.gz
 man/man3/BL_SAM_SEQ.3.gz
 man/man3/BL_SAM_SEQ_AE.3.gz
+man/man3/BL_SAM_SEQ_ARRAY_SIZE.3.gz
 man/man3/BL_SAM_SEQ_LEN.3.gz
 man/man3/BL_SAM_TLEN.3.gz
 man/man3/BL_VCF_ALT.3.gz
@@ -192,16 +200,22 @@ man/man3/BL_VCF_FILTER.3.gz
 man/man3/BL_VCF_FILTER_AE.3.gz
 man/man3/BL_VCF_FORMAT.3.gz
 man/man3/BL_VCF_FORMAT_AE.3.gz
+man/man3/BL_VCF_FORMAT_ARRAY_SIZE.3.gz
 man/man3/BL_VCF_FORMAT_LEN.3.gz
-man/man3/BL_VCF_FORMAT_MAX.3.gz
 man/man3/BL_VCF_ID.3.gz
 man/man3/BL_VCF_ID_AE.3.gz
 man/man3/BL_VCF_INFO.3.gz
 man/man3/BL_VCF_INFO_AE.3.gz
+man/man3/BL_VCF_INFO_ARRAY_SIZE.3.gz
 man/man3/BL_VCF_INFO_LEN.3.gz
-man/man3/BL_VCF_INFO_MAX.3.gz
 man/man3/BL_VCF_MULTI_SAMPLES.3.gz
 man/man3/BL_VCF_MULTI_SAMPLES_AE.3.gz
+man/man3/BL_VCF_MULTI_SAMPLE_ARRAY_SIZES.3.gz
+man/man3/BL_VCF_MULTI_SAMPLE_ARRAY_SIZES_AE.3.gz
+man/man3/BL_VCF_MULTI_SAMPLE_COUNT.3.gz
+man/man3/BL_VCF_MULTI_SAMPLE_LENS.3.gz
+man/man3/BL_VCF_MULTI_SAMPLE_LENS_AE.3.gz
+man/man3/BL_VCF_MULTI_SAMPLE_POINTER_ARRAY_SIZE.3.gz
 man/man3/BL_VCF_OTHER_COUNT.3.gz
 man/man3/BL_VCF_PHREDS.3.gz
 man/man3/BL_VCF_PHREDS_AE.3.gz
@@ -213,9 +227,13 @@ man/man3/BL_VCF_QUAL_AE.3.gz
 man/man3/BL_VCF_REF.3.gz
 man/man3/BL_VCF_REF_AE.3.gz
 man/man3/BL_VCF_REF_COUNT.3.gz
+man/man3/BL_VCF_SAMPLE_ARRAY_SIZE.3.gz
+man/man3/BL_VCF_SAMPLE_LEN.3.gz
 man/man3/BL_VCF_SAMPLE_MAX.3.gz
 man/man3/BL_VCF_SINGLE_SAMPLE.3.gz
 man/man3/BL_VCF_SINGLE_SAMPLE_AE.3.gz
+man/man3/BL_VCF_SINGLE_SAMPLE_ARRAY_SIZE.3.gz
+man/man3/BL_VCF_SINGLE_SAMPLE_LEN.3.gz
 man/man3/biolibc.3.gz
 man/man3/bl_align_map_seq_exact.3.gz
 man/man3/bl_align_map_seq_sub.3.gz
@@ -303,7 +321,9 @@ man/man3/bl_fastx_set_fasta.3.gz
 man/man3/bl_fastx_set_fastq.3.gz
 man/man3/bl_fastx_set_format.3.gz
 man/man3/bl_fastx_write.3.gz
+man/man3/bl_gff_copy.3.gz
 man/man3/bl_gff_copy_header.3.gz
+man/man3/bl_gff_dup.3.gz
 man/man3/bl_gff_extract_attribute.3.gz
 man/man3/bl_gff_free.3.gz
 man/man3/bl_gff_index_add.3.gz
@@ -324,9 +344,13 @@ man/man3/bl_gff_index_set_start_ae.3.gz
 man/man3/bl_gff_index_set_start_cpy.3.gz
 man/man3/bl_gff_init.3.gz
 man/man3/bl_gff_read.3.gz
+man/man3/bl_gff_sam_cmp.3.gz
+man/man3/bl_gff_sam_overlap.3.gz
 man/man3/bl_gff_set_attributes.3.gz
 man/man3/bl_gff_set_attributes_ae.3.gz
+man/man3/bl_gff_set_attributes_array_size.3.gz
 man/man3/bl_gff_set_attributes_cpy.3.gz
+man/man3/bl_gff_set_attributes_len.3.gz
 man/man3/bl_gff_set_end.3.gz
 man/man3/bl_gff_set_feature_id.3.gz
 man/man3/bl_gff_set_feature_id_ae.3.gz
@@ -334,6 +358,9 @@ man/man3/bl_gff_set_feature_id_cpy.3.gz
 man/man3/bl_gff_set_feature_name.3.gz
 man/man3/bl_gff_set_feature_name_ae.3.gz
 man/man3/bl_gff_set_feature_name_cpy.3.gz
+man/man3/bl_gff_set_feature_parent.3.gz
+man/man3/bl_gff_set_feature_parent_ae.3.gz
+man/man3/bl_gff_set_feature_parent_cpy.3.gz
 man/man3/bl_gff_set_file_pos.3.gz
 man/man3/bl_gff_set_gene_name_cpy.3.gz
 man/man3/bl_gff_set_phase.3.gz
@@ -399,11 +426,19 @@ man/man3/bl_sam_buff_set_trailing_alignments.3.gz
 man/man3/bl_sam_buff_set_unmapped_alignments.3.gz
 man/man3/bl_sam_buff_shift.3.gz
 man/man3/bl_sam_copy.3.gz
+man/man3/bl_sam_copy_header.3.gz
+man/man3/bl_sam_fclose.3.gz
+man/man3/bl_sam_fopen.3.gz
 man/man3/bl_sam_free.3.gz
+man/man3/bl_sam_gff_cmp.3.gz
+man/man3/bl_sam_gff_overlap.3.gz
 man/man3/bl_sam_init.3.gz
 man/man3/bl_sam_read.3.gz
+man/man3/bl_sam_set_cigar.3.gz
 man/man3/bl_sam_set_cigar_ae.3.gz
+man/man3/bl_sam_set_cigar_array_size.3.gz
 man/man3/bl_sam_set_cigar_cpy.3.gz
+man/man3/bl_sam_set_cigar_len.3.gz
 man/man3/bl_sam_set_flag.3.gz
 man/man3/bl_sam_set_mapq.3.gz
 man/man3/bl_sam_set_pnext.3.gz
@@ -412,6 +447,7 @@ man/man3/bl_sam_set_qname_ae.3.gz
 man/man3/bl_sam_set_qname_cpy.3.gz
 man/man3/bl_sam_set_qual.3.gz
 man/man3/bl_sam_set_qual_ae.3.gz
+man/man3/bl_sam_set_qual_array_size.3.gz
 man/man3/bl_sam_set_qual_cpy.3.gz
 man/man3/bl_sam_set_qual_len.3.gz
 man/man3/bl_sam_set_rname_ae.3.gz
@@ -420,9 +456,11 @@ man/man3/bl_sam_set_rnext_ae.3.gz
 man/man3/bl_sam_set_rnext_cpy.3.gz
 man/man3/bl_sam_set_seq.3.gz
 man/man3/bl_sam_set_seq_ae.3.gz
+man/man3/bl_sam_set_seq_array_size.3.gz
 man/man3/bl_sam_set_seq_cpy.3.gz
 man/man3/bl_sam_set_seq_len.3.gz
 man/man3/bl_sam_set_tlen.3.gz
+man/man3/bl_sam_skip_header.3.gz
 man/man3/bl_sam_write.3.gz
 man/man3/bl_vcf_call_downstream_of_alignment.3.gz
 man/man3/bl_vcf_call_in_alignment.3.gz
@@ -433,7 +471,6 @@ man/man3/bl_vcf_init.3.gz
 man/man3/bl_vcf_parse_field_spec.3.gz
 man/man3/bl_vcf_read_ss_call.3.gz
 man/man3/bl_vcf_read_static_fields.3.gz
-man/man3/bl_vcf_sample_alloc.3.gz
 man/man3/bl_vcf_set_alt_ae.3.gz
 man/man3/bl_vcf_set_alt_count.3.gz
 man/man3/bl_vcf_set_alt_cpy.3.gz
@@ -443,16 +480,24 @@ man/man3/bl_vcf_set_filter_ae.3.gz
 man/man3/bl_vcf_set_filter_cpy.3.gz
 man/man3/bl_vcf_set_format.3.gz
 man/man3/bl_vcf_set_format_ae.3.gz
+man/man3/bl_vcf_set_format_array_size.3.gz
 man/man3/bl_vcf_set_format_cpy.3.gz
 man/man3/bl_vcf_set_format_len.3.gz
-man/man3/bl_vcf_set_format_max.3.gz
 man/man3/bl_vcf_set_id_ae.3.gz
 man/man3/bl_vcf_set_id_cpy.3.gz
 man/man3/bl_vcf_set_info.3.gz
 man/man3/bl_vcf_set_info_ae.3.gz
+man/man3/bl_vcf_set_info_array_size.3.gz
 man/man3/bl_vcf_set_info_cpy.3.gz
 man/man3/bl_vcf_set_info_len.3.gz
-man/man3/bl_vcf_set_info_max.3.gz
+man/man3/bl_vcf_set_multi_sample_array_sizes.3.gz
+man/man3/bl_vcf_set_multi_sample_array_sizes_ae.3.gz
+man/man3/bl_vcf_set_multi_sample_array_sizes_cpy.3.gz
+man/man3/bl_vcf_set_multi_sample_count.3.gz
+man/man3/bl_vcf_set_multi_sample_lens.3.gz
+man/man3/bl_vcf_set_multi_sample_lens_ae.3.gz
+man/man3/bl_vcf_set_multi_sample_lens_cpy.3.gz
+man/man3/bl_vcf_set_multi_sample_pointer_array_size.3.gz
 man/man3/bl_vcf_set_multi_samples.3.gz
 man/man3/bl_vcf_set_multi_samples_ae.3.gz
 man/man3/bl_vcf_set_multi_samples_cpy.3.gz
@@ -468,10 +513,12 @@ man/man3/bl_vcf_set_qual_cpy.3.gz
 man/man3/bl_vcf_set_ref_ae.3.gz
 man/man3/bl_vcf_set_ref_count.3.gz
 man/man3/bl_vcf_set_ref_cpy.3.gz
-man/man3/bl_vcf_set_sample_max.3.gz
 man/man3/bl_vcf_set_single_sample.3.gz
 man/man3/bl_vcf_set_single_sample_ae.3.gz
+man/man3/bl_vcf_set_single_sample_array_size.3.gz
 man/man3/bl_vcf_set_single_sample_cpy.3.gz
+man/man3/bl_vcf_set_single_sample_len.3.gz
+man/man3/bl_vcf_skip_header.3.gz
 man/man3/bl_vcf_skip_meta_data.3.gz
 man/man3/bl_vcf_write_ss_call.3.gz
 man/man3/bl_vcf_write_static_fields.3.gz