[pkgsrc/trunk]: pkgsrc/biology/biolibc biology/biolibc: Update to 0.2.2

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

details:   https://anonhg.NetBSD.org/pkgsrc/rev/117ecd0b8ec5
branches:  trunk
changeset: 375554:117ecd0b8ec5
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Tue Mar 15 21:06:32 2022 +0000

description:
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

diffstat:

 biology/biolibc/Makefile      |    4 +-
 biology/biolibc/PLIST         |  118 +++++++++++++++++++++++++++++++++++++----
 biology/biolibc/buildlink3.mk |    4 +-
 biology/biolibc/distinfo      |    8 +-
 4 files changed, 113 insertions(+), 21 deletions(-)

diffs (269 lines):

diff -r ad884cdd9099 -r 117ecd0b8ec5 biology/biolibc/Makefile
--- a/biology/biolibc/Makefile  Tue Mar 15 21:03:36 2022 +0000
+++ b/biology/biolibc/Makefile  Tue Mar 15 21:06:32 2022 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.7 2021/12/14 18:58:56 bacon Exp $
+# $NetBSD: Makefile,v 1.8 2022/03/15 21:06:32 bacon Exp $
 
-DISTNAME=      biolibc-0.2.1
+DISTNAME=      biolibc-0.2.2
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
 
diff -r ad884cdd9099 -r 117ecd0b8ec5 biology/biolibc/PLIST
--- a/biology/biolibc/PLIST     Tue Mar 15 21:03:36 2022 +0000
+++ b/biology/biolibc/PLIST     Tue Mar 15 21:06:32 2022 +0000
@@ -1,21 +1,61 @@
-@comment $NetBSD: PLIST,v 1.7 2021/12/14 18:58:56 bacon Exp $
+@comment $NetBSD: PLIST,v 1.8 2022/03/15 21:06:32 bacon Exp $
+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
+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
@@ -58,23 +98,39 @@
 man/man3/BL_FASTQ_SEQ_AE.3
 man/man3/BL_FASTQ_SEQ_ARRAY_SIZE.3
 man/man3/BL_FASTQ_SEQ_LEN.3
+man/man3/BL_FASTX_FASTA.3
+man/man3/BL_FASTX_FASTQ.3
+man/man3/BL_FASTX_FORMAT.3
+man/man3/BL_FASTX_UNION.3
+man/man3/BL_FASTX_}.3
 man/man3/BL_GFF_ATTRIBUTES.3
 man/man3/BL_GFF_ATTRIBUTES_AE.3
 man/man3/BL_GFF_END.3
-man/man3/BL_GFF_FEATURE.3
-man/man3/BL_GFF_FEATURE_AE.3
 man/man3/BL_GFF_FEATURE_ID.3
 man/man3/BL_GFF_FEATURE_ID_AE.3
-man/man3/BL_GFF_GENE_NAME.3
-man/man3/BL_GFF_GENE_NAME_AE.3
+man/man3/BL_GFF_FEATURE_NAME.3
+man/man3/BL_GFF_FEATURE_NAME_AE.3
+man/man3/BL_GFF_FILE_POS.3
+man/man3/BL_GFF_INDEX_ARRAY_SIZE.3
+man/man3/BL_GFF_INDEX_COUNT.3
+man/man3/BL_GFF_INDEX_END.3
+man/man3/BL_GFF_INDEX_END_AE.3
+man/man3/BL_GFF_INDEX_FILE_POS.3
+man/man3/BL_GFF_INDEX_FILE_POS_AE.3
+man/man3/BL_GFF_INDEX_SEQID.3
+man/man3/BL_GFF_INDEX_SEQID_AE.3
+man/man3/BL_GFF_INDEX_START.3
+man/man3/BL_GFF_INDEX_START_AE.3
 man/man3/BL_GFF_PHASE.3
 man/man3/BL_GFF_SCORE.3
-man/man3/BL_GFF_SEQUENCE.3
-man/man3/BL_GFF_SEQUENCE_AE.3
+man/man3/BL_GFF_SEQID.3
+man/man3/BL_GFF_SEQID_AE.3
 man/man3/BL_GFF_SOURCE.3
 man/man3/BL_GFF_SOURCE_AE.3
 man/man3/BL_GFF_START.3
 man/man3/BL_GFF_STRAND.3
+man/man3/BL_GFF_TYPE.3
+man/man3/BL_GFF_TYPE_AE.3
 man/man3/BL_OVERLAP_FEATURE1_LEN.3
 man/man3/BL_OVERLAP_FEATURE2_LEN.3
 man/man3/BL_OVERLAP_OVERLAP_END.3
@@ -98,6 +154,7 @@
 man/man3/BL_SAM_BUFF_MAPQ_LOW.3
 man/man3/BL_SAM_BUFF_MAPQ_MIN.3
 man/man3/BL_SAM_BUFF_MAPQ_SUM.3
+man/man3/BL_SAM_BUFF_MAX_ALIGNMENTS.3
 man/man3/BL_SAM_BUFF_MAX_COUNT.3
 man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3
 man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3
@@ -136,6 +193,7 @@
 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_LEN.3
 man/man3/BL_VCF_FORMAT_MAX.3
 man/man3/BL_VCF_ID.3
 man/man3/BL_VCF_ID_AE.3
@@ -160,6 +218,10 @@
 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
@@ -200,8 +262,11 @@
 man/man3/bl_fasta_set_seq_cpy.3
 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_free.3
 man/man3/bl_fastq_init.3
+man/man3/bl_fastq_name_cmp.3
 man/man3/bl_fastq_read.3
 man/man3/bl_fastq_set_desc.3
 man/man3/bl_fastq_set_desc_ae.3
@@ -235,28 +300,53 @@
 man/man3/bl_fastx_read.3
 man/man3/bl_fastx_seq.3
 man/man3/bl_fastx_seq_len.3
+man/man3/bl_fastx_set_fasta.3
+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_header.3
+man/man3/bl_gff_extract_attribute.3
+man/man3/bl_gff_free.3
+man/man3/bl_gff_index_add.3
+man/man3/bl_gff_index_seek_reverse.3
+man/man3/bl_gff_index_set_array_size.3
+man/man3/bl_gff_index_set_count.3
+man/man3/bl_gff_index_set_end.3
+man/man3/bl_gff_index_set_end_ae.3
+man/man3/bl_gff_index_set_end_cpy.3
+man/man3/bl_gff_index_set_file_pos.3
+man/man3/bl_gff_index_set_file_pos_ae.3
+man/man3/bl_gff_index_set_file_pos_cpy.3
+man/man3/bl_gff_index_set_seqid.3
+man/man3/bl_gff_index_set_seqid_ae.3
+man/man3/bl_gff_index_set_seqid_cpy.3
+man/man3/bl_gff_index_set_start.3
+man/man3/bl_gff_index_set_start_ae.3
+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_set_attributes.3
 man/man3/bl_gff_set_attributes_ae.3
 man/man3/bl_gff_set_attributes_cpy.3
 man/man3/bl_gff_set_end.3
-man/man3/bl_gff_set_feature_ae.3
-man/man3/bl_gff_set_feature_cpy.3
 man/man3/bl_gff_set_feature_id.3
 man/man3/bl_gff_set_feature_id_ae.3
 man/man3/bl_gff_set_feature_id_cpy.3
-man/man3/bl_gff_set_gene_name.3
-man/man3/bl_gff_set_gene_name_ae.3
+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_file_pos.3
 man/man3/bl_gff_set_gene_name_cpy.3
 man/man3/bl_gff_set_phase.3
 man/man3/bl_gff_set_score.3
-man/man3/bl_gff_set_sequence_ae.3
-man/man3/bl_gff_set_sequence_cpy.3
+man/man3/bl_gff_set_seqid_ae.3
+man/man3/bl_gff_set_seqid_cpy.3
 man/man3/bl_gff_set_source_ae.3
 man/man3/bl_gff_set_source_cpy.3
 man/man3/bl_gff_set_start.3
 man/man3/bl_gff_set_strand.3
+man/man3/bl_gff_set_type_ae.3
+man/man3/bl_gff_set_type_cpy.3
 man/man3/bl_gff_skip_header.3
 man/man3/bl_gff_to_bed.3
 man/man3/bl_gff_write.3
@@ -297,6 +387,7 @@
 man/man3/bl_sam_buff_set_mapq_low.3
 man/man3/bl_sam_buff_set_mapq_min.3
 man/man3/bl_sam_buff_set_mapq_sum.3
+man/man3/bl_sam_buff_set_max_alignments.3
 man/man3/bl_sam_buff_set_max_count.3
 man/man3/bl_sam_buff_set_max_discarded_score.3
 man/man3/bl_sam_buff_set_min_discarded_score.3
@@ -354,6 +445,7 @@
 man/man3/bl_vcf_set_format.3
 man/man3/bl_vcf_set_format_ae.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
diff -r ad884cdd9099 -r 117ecd0b8ec5 biology/biolibc/buildlink3.mk
--- a/biology/biolibc/buildlink3.mk     Tue Mar 15 21:03:36 2022 +0000
+++ b/biology/biolibc/buildlink3.mk     Tue Mar 15 21:06:32 2022 +0000
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.7 2021/12/14 18:58:57 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.8 2022/03/15 21:06:32 bacon Exp $
 
 BUILDLINK_TREE+=       biolibc
 
 .if !defined(BIOLIBC_BUILDLINK3_MK)
 BIOLIBC_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.2.1
+BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.2.2
 BUILDLINK_PKGSRCDIR.biolibc?=  ../../biology/biolibc
 
 .include "../../devel/libxtend/buildlink3.mk"
diff -r ad884cdd9099 -r 117ecd0b8ec5 biology/biolibc/distinfo
--- a/biology/biolibc/distinfo  Tue Mar 15 21:03:36 2022 +0000
+++ b/biology/biolibc/distinfo  Tue Mar 15 21:06:32 2022 +0000
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.9 2021/12/14 18:58:57 bacon Exp $
+$NetBSD: distinfo,v 1.10 2022/03/15 21:06:32 bacon Exp $
 
-BLAKE2s (biolibc-0.2.1.tar.gz) = e81198c3ae3185592c58cdd72b046db0bce898845bf4f850a46a35c2cadb09b6
-SHA512 (biolibc-0.2.1.tar.gz) = 0743199591e6f3b8ea9986bbddcba972538925787aa01463236d9c7ec809860eb2ee5174bbc8f00d04e33d1802f7ff87f0d4fb010a21cb3a2eb6bb1978cb2647
-Size (biolibc-0.2.1.tar.gz) = 104282 bytes
+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