biology/biolibc: Update to 0.2.2

Numerous bug fixes and enhancements
Serveral new functions
3 new classes
Cleaned up some API slop
Changes: https://github.com/auerlab/biolibc/tags

3 files changed, 108 insertions, 16 deletions

diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile
index b9e0322a1721..465f7ea9a665 100644
--- a/biology/biolibc/Makefile
+++ b/biology/biolibc/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	biolibc
-DISTVERSION=	0.2.1
+DISTVERSION=	0.2.2
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo
index a578ca9874ea..c319bf83d1ed 100644
--- a/biology/biolibc/distinfo
+++ b/biology/biolibc/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1639331819
-SHA256 (auerlab-biolibc-0.2.1_GH0.tar.gz) = c3a3ac20c549a7a7626c77bdb86e81bc01ece864c2818a1fa744614e81f9eda3
-SIZE (auerlab-biolibc-0.2.1_GH0.tar.gz) = 104282
+TIMESTAMP = 1647347323
+SHA256 (auerlab-biolibc-0.2.2_GH0.tar.gz) = b2d8ef23ce93321cc624fb1c7851e1353b12ac89ec0bac6a4f9ae0f3648869e4
+SIZE (auerlab-biolibc-0.2.2_GH0.tar.gz) = 129251
diff --git a/biology/biolibc/pkg-plist b/biology/biolibc/pkg-plist
index e8cce147332e..c0167ab0df06 100644
--- a/biology/biolibc/pkg-plist
+++ b/biology/biolibc/pkg-plist
@@ -1,20 +1,60 @@
+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
 include/biolibc/bed.h
 include/biolibc/biolibc.h
 include/biolibc/biostring.h
+include/biolibc/fasta-accessors.h
+include/biolibc/fasta-mutators.h
+include/biolibc/fasta-rvs.h
 include/biolibc/fasta.h
+include/biolibc/fastq-accessors.h
+include/biolibc/fastq-mutators.h
+include/biolibc/fastq-rvs.h
 include/biolibc/fastq.h
+include/biolibc/fastx-accessors.h
+include/biolibc/fastx-mutators.h
+include/biolibc/fastx-rvs.h
 include/biolibc/fastx.h
+include/biolibc/gff-accessors.h
+include/biolibc/gff-index-accessors.h
+include/biolibc/gff-index-mutators.h
+include/biolibc/gff-index-rvs.h
+include/biolibc/gff-index.h
+include/biolibc/gff-mutators.h
+include/biolibc/gff-rvs.h
 include/biolibc/gff.h
+include/biolibc/overlap-accessors.h
+include/biolibc/overlap-mutators.h
+include/biolibc/overlap-rvs.h
 include/biolibc/overlap.h
+include/biolibc/pos-list-accessors.h
+include/biolibc/pos-list-mutators.h
+include/biolibc/pos-list-rvs.h
 include/biolibc/pos-list.h
+include/biolibc/sam-accessors.h
+include/biolibc/sam-buff-accessors.h
+include/biolibc/sam-buff-mutators.h
+include/biolibc/sam-buff-rvs.h
 include/biolibc/sam-buff.h
+include/biolibc/sam-mutators.h
+include/biolibc/sam-rvs.h
 include/biolibc/sam.h
 include/biolibc/translate.h
+include/biolibc/vcf-accessors.h
+include/biolibc/vcf-mutators.h
+include/biolibc/vcf-rvs.h
 include/biolibc/vcf.h
 lib/libbiolibc.a
 lib/libbiolibc.so
 lib/libbiolibc.so.2
 lib/libbiolibc.so.2.0
+man/man3/BL_ALIGN_MAX_MISMATCH_PERCENT.3.gz
+man/man3/BL_ALIGN_MIN_MATCH.3.gz
 man/man3/BL_BED_BLOCK_COUNT.3.gz
 man/man3/BL_BED_BLOCK_SIZES.3.gz
 man/man3/BL_BED_BLOCK_SIZES_AE.3.gz
@@ -57,23 +97,39 @@ man/man3/BL_FASTQ_SEQ.3.gz
 man/man3/BL_FASTQ_SEQ_AE.3.gz
 man/man3/BL_FASTQ_SEQ_ARRAY_SIZE.3.gz
 man/man3/BL_FASTQ_SEQ_LEN.3.gz
+man/man3/BL_FASTX_FASTA.3.gz
+man/man3/BL_FASTX_FASTQ.3.gz
+man/man3/BL_FASTX_FORMAT.3.gz
+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_END.3.gz
-man/man3/BL_GFF_FEATURE.3.gz
-man/man3/BL_GFF_FEATURE_AE.3.gz
 man/man3/BL_GFF_FEATURE_ID.3.gz
 man/man3/BL_GFF_FEATURE_ID_AE.3.gz
-man/man3/BL_GFF_GENE_NAME.3.gz
-man/man3/BL_GFF_GENE_NAME_AE.3.gz
+man/man3/BL_GFF_FEATURE_NAME.3.gz
+man/man3/BL_GFF_FEATURE_NAME_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
+man/man3/BL_GFF_INDEX_END.3.gz
+man/man3/BL_GFF_INDEX_END_AE.3.gz
+man/man3/BL_GFF_INDEX_FILE_POS.3.gz
+man/man3/BL_GFF_INDEX_FILE_POS_AE.3.gz
+man/man3/BL_GFF_INDEX_SEQID.3.gz
+man/man3/BL_GFF_INDEX_SEQID_AE.3.gz
+man/man3/BL_GFF_INDEX_START.3.gz
+man/man3/BL_GFF_INDEX_START_AE.3.gz
 man/man3/BL_GFF_PHASE.3.gz
 man/man3/BL_GFF_SCORE.3.gz
-man/man3/BL_GFF_SEQUENCE.3.gz
-man/man3/BL_GFF_SEQUENCE_AE.3.gz
+man/man3/BL_GFF_SEQID.3.gz
+man/man3/BL_GFF_SEQID_AE.3.gz
 man/man3/BL_GFF_SOURCE.3.gz
 man/man3/BL_GFF_SOURCE_AE.3.gz
 man/man3/BL_GFF_START.3.gz
 man/man3/BL_GFF_STRAND.3.gz
+man/man3/BL_GFF_TYPE.3.gz
+man/man3/BL_GFF_TYPE_AE.3.gz
 man/man3/BL_OVERLAP_FEATURE1_LEN.3.gz
 man/man3/BL_OVERLAP_FEATURE2_LEN.3.gz
 man/man3/BL_OVERLAP_OVERLAP_END.3.gz
@@ -97,6 +153,7 @@ man/man3/BL_SAM_BUFF_MAPQ_HIGH.3.gz
 man/man3/BL_SAM_BUFF_MAPQ_LOW.3.gz
 man/man3/BL_SAM_BUFF_MAPQ_MIN.3.gz
 man/man3/BL_SAM_BUFF_MAPQ_SUM.3.gz
+man/man3/BL_SAM_BUFF_MAX_ALIGNMENTS.3.gz
 man/man3/BL_SAM_BUFF_MAX_COUNT.3.gz
 man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3.gz
 man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3.gz
@@ -135,6 +192,7 @@ 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_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
@@ -159,6 +217,10 @@ 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/biolibc.3.gz
+man/man3/bl_align_map_seq_exact.3.gz
+man/man3/bl_align_map_seq_sub.3.gz
+man/man3/bl_align_set_max_mismatch_percent.3.gz
+man/man3/bl_align_set_min_match.3.gz
 man/man3/bl_bed_check_order.3.gz
 man/man3/bl_bed_gff_cmp.3.gz
 man/man3/bl_bed_read.3.gz
@@ -199,8 +261,11 @@ man/man3/bl_fasta_set_seq_array_size.3.gz
 man/man3/bl_fasta_set_seq_cpy.3.gz
 man/man3/bl_fasta_set_seq_len.3.gz
 man/man3/bl_fasta_write.3.gz
+man/man3/bl_fastq_3p_trim.3.gz
+man/man3/bl_fastq_find_3p_low_qual.3.gz
 man/man3/bl_fastq_free.3.gz
 man/man3/bl_fastq_init.3.gz
+man/man3/bl_fastq_name_cmp.3.gz
 man/man3/bl_fastq_read.3.gz
 man/man3/bl_fastq_set_desc.3.gz
 man/man3/bl_fastq_set_desc_ae.3.gz
@@ -234,28 +299,53 @@ man/man3/bl_fastx_qual_len.3.gz
 man/man3/bl_fastx_read.3.gz
 man/man3/bl_fastx_seq.3.gz
 man/man3/bl_fastx_seq_len.3.gz
+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_header.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
+man/man3/bl_gff_index_seek_reverse.3.gz
+man/man3/bl_gff_index_set_array_size.3.gz
+man/man3/bl_gff_index_set_count.3.gz
+man/man3/bl_gff_index_set_end.3.gz
+man/man3/bl_gff_index_set_end_ae.3.gz
+man/man3/bl_gff_index_set_end_cpy.3.gz
+man/man3/bl_gff_index_set_file_pos.3.gz
+man/man3/bl_gff_index_set_file_pos_ae.3.gz
+man/man3/bl_gff_index_set_file_pos_cpy.3.gz
+man/man3/bl_gff_index_set_seqid.3.gz
+man/man3/bl_gff_index_set_seqid_ae.3.gz
+man/man3/bl_gff_index_set_seqid_cpy.3.gz
+man/man3/bl_gff_index_set_start.3.gz
+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_set_attributes.3.gz
 man/man3/bl_gff_set_attributes_ae.3.gz
 man/man3/bl_gff_set_attributes_cpy.3.gz
 man/man3/bl_gff_set_end.3.gz
-man/man3/bl_gff_set_feature_ae.3.gz
-man/man3/bl_gff_set_feature_cpy.3.gz
 man/man3/bl_gff_set_feature_id.3.gz
 man/man3/bl_gff_set_feature_id_ae.3.gz
 man/man3/bl_gff_set_feature_id_cpy.3.gz
-man/man3/bl_gff_set_gene_name.3.gz
-man/man3/bl_gff_set_gene_name_ae.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_file_pos.3.gz
 man/man3/bl_gff_set_gene_name_cpy.3.gz
 man/man3/bl_gff_set_phase.3.gz
 man/man3/bl_gff_set_score.3.gz
-man/man3/bl_gff_set_sequence_ae.3.gz
-man/man3/bl_gff_set_sequence_cpy.3.gz
+man/man3/bl_gff_set_seqid_ae.3.gz
+man/man3/bl_gff_set_seqid_cpy.3.gz
 man/man3/bl_gff_set_source_ae.3.gz
 man/man3/bl_gff_set_source_cpy.3.gz
 man/man3/bl_gff_set_start.3.gz
 man/man3/bl_gff_set_strand.3.gz
+man/man3/bl_gff_set_type_ae.3.gz
+man/man3/bl_gff_set_type_cpy.3.gz
 man/man3/bl_gff_skip_header.3.gz
 man/man3/bl_gff_to_bed.3.gz
 man/man3/bl_gff_write.3.gz
@@ -296,6 +386,7 @@ man/man3/bl_sam_buff_set_mapq_high.3.gz
 man/man3/bl_sam_buff_set_mapq_low.3.gz
 man/man3/bl_sam_buff_set_mapq_min.3.gz
 man/man3/bl_sam_buff_set_mapq_sum.3.gz
+man/man3/bl_sam_buff_set_max_alignments.3.gz
 man/man3/bl_sam_buff_set_max_count.3.gz
 man/man3/bl_sam_buff_set_max_discarded_score.3.gz
 man/man3/bl_sam_buff_set_min_discarded_score.3.gz
@@ -353,6 +444,7 @@ 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_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