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biolibc: Update to 0.1.3.43
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Sat Jul 17 15:11:02 2021 -0500
Changeset: b11c4c5dfc8d43434778f82a615b50713d0ede2e
Modified Files:
biolibc/Makefile
biolibc/PLIST
biolibc/buildlink3.mk
biolibc/distinfo
Log Message:
biolibc: Update to 0.1.3.43
Major API overhaul
Generate accessor and mutator macros for all structure members
Prefix functioins/macros with bl_
Generate man pages for all functions and macros
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=b11c4c5dfc8d43434778f82a615b50713d0ede2e
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 | 282 ++++++++++++++++++++++++++++++++++++++------------
biolibc/buildlink3.mk | 2 +-
biolibc/distinfo | 8 +-
4 files changed, 224 insertions(+), 72 deletions(-)
diffs:
diff --git a/biolibc/Makefile b/biolibc/Makefile
index cca0d809d5..8c93771e2c 100644
--- a/biolibc/Makefile
+++ b/biolibc/Makefile
@@ -1,9 +1,9 @@
# $NetBSD$
-DISTNAME= biolibc-0.1.3.21
+DISTNAME= biolibc-0.1.3.43
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG= 6b5ac39edda905980da19042afe1e3e46d92d432
+GITHUB_TAG= d1d99c030d9b6b4e36b868f449e8de7d13188de8
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://github.com/auerlab/biolibc
diff --git a/biolibc/PLIST b/biolibc/PLIST
index 6422d3290c..68f82291fa 100644
--- a/biolibc/PLIST
+++ b/biolibc/PLIST
@@ -1,10 +1,9 @@
@comment $NetBSD$
include/biolibc/bed.h
-include/biolibc/bio-overlap.h
include/biolibc/biolibc.h
include/biolibc/biostring.h
-include/biolibc/dsv.h
include/biolibc/gff.h
+include/biolibc/overlap.h
include/biolibc/pos-list.h
include/biolibc/sam-buff.h
include/biolibc/sam.h
@@ -13,67 +12,220 @@ lib/libbiolibc.a
lib/libbiolibc.so
lib/libbiolibc.so.2
lib/libbiolibc.so.2.0
-man/man3/bed_check_order.3
-man/man3/bed_gff_cmp.3
-man/man3/bed_read_feature.3
-man/man3/bed_set_chromosome.3
-man/man3/bed_set_end_pos.3
-man/man3/bed_set_fields.3
-man/man3/bed_set_name.3
-man/man3/bed_set_rgb_str.3
-man/man3/bed_set_score.3
-man/man3/bed_set_start_pos.3
-man/man3/bed_set_strand.3
-man/man3/bed_set_thick_end_pos.3
-man/man3/bed_set_thick_start_pos.3
-man/man3/bed_skip_header.3
-man/man3/bed_write_feature.3
-man/man3/bio_overlap_print.3
-man/man3/bio_overlap_set_all.3
+man/man3/BL_BED_BLOCK_COUNT.3
+man/man3/BL_BED_BLOCK_SIZES.3
+man/man3/BL_BED_BLOCK_STARTS.3
+man/man3/BL_BED_CHROMOSOME.3
+man/man3/BL_BED_END_POS.3
+man/man3/BL_BED_FIELDS.3
+man/man3/BL_BED_NAME.3
+man/man3/BL_BED_RGB_STR.3
+man/man3/BL_BED_SCORE.3
+man/man3/BL_BED_SET_BLOCK_COUNT.3
+man/man3/BL_BED_SET_BLOCK_SIZES.3
+man/man3/BL_BED_SET_BLOCK_STARTS.3
+man/man3/BL_BED_SET_CHROMOSOME.3
+man/man3/BL_BED_SET_END_POS.3
+man/man3/BL_BED_SET_FIELDS.3
+man/man3/BL_BED_SET_NAME.3
+man/man3/BL_BED_SET_RGB_STR.3
+man/man3/BL_BED_SET_SCORE.3
+man/man3/BL_BED_SET_START_POS.3
+man/man3/BL_BED_SET_STRAND.3
+man/man3/BL_BED_SET_THICK_END_POS.3
+man/man3/BL_BED_SET_THICK_START_POS.3
+man/man3/BL_BED_START_POS.3
+man/man3/BL_BED_STRAND.3
+man/man3/BL_BED_THICK_END_POS.3
+man/man3/BL_BED_THICK_START_POS.3
+man/man3/BL_GFF_ATTRIBUTES.3
+man/man3/BL_GFF_END_POS.3
+man/man3/BL_GFF_FEATURE_ID.3
+man/man3/BL_GFF_GANE_NAME.3
+man/man3/BL_GFF_GENE_NAME.3
+man/man3/BL_GFF_NAME.3
+man/man3/BL_GFF_PHASE.3
+man/man3/BL_GFF_SCORE.3
+man/man3/BL_GFF_SEQUENCE.3
+man/man3/BL_GFF_SET_ATTRIBUTES.3
+man/man3/BL_GFF_SET_END_POS.3
+man/man3/BL_GFF_SET_FEATURE_ID.3
+man/man3/BL_GFF_SET_GANE_NAME.3
+man/man3/BL_GFF_SET_GENE_NAME.3
+man/man3/BL_GFF_SET_NAME.3
+man/man3/BL_GFF_SET_PHASE.3
+man/man3/BL_GFF_SET_SCORE.3
+man/man3/BL_GFF_SET_SEQUENCE.3
+man/man3/BL_GFF_SET_SOURCE.3
+man/man3/BL_GFF_SET_START_POS,.3
+man/man3/BL_GFF_SET_START_POS.3
+man/man3/BL_GFF_SET_STRAND.3
+man/man3/BL_GFF_SOURCE.3
+man/man3/BL_GFF_START_POS,.3
+man/man3/BL_GFF_START_POS.3
+man/man3/BL_GFF_STRAND.3
+man/man3/BL_OVERLAP_FEATURE1_LEN.3
+man/man3/BL_OVERLAP_FEATURE2_LEN.3
+man/man3/BL_OVERLAP_OVERLAP_END.3
+man/man3/BL_OVERLAP_OVERLAP_LEN.3
+man/man3/BL_OVERLAP_OVERLAP_START.3
+man/man3/BL_OVERLAP_SET_FEATURE1_LEN.3
+man/man3/BL_OVERLAP_SET_FEATURE2_LEN.3
+man/man3/BL_OVERLAP_SET_OVERLAP_END.3
+man/man3/BL_OVERLAP_SET_OVERLAP_LEN.3
+man/man3/BL_OVERLAP_SET_OVERLAP_START.3
+man/man3/BL_POS_LIST_ARRAY_SIZE.3
+man/man3/BL_POS_LIST_COUNT.3
+man/man3/BL_POS_LIST_POSITIONS.3
+man/man3/BL_POS_LIST_SET_ARRAY_SIZE.3
+man/man3/BL_POS_LIST_SET_COUNT.3
+man/man3/BL_POS_LIST_SET_POSITIONS.3
+man/man3/BL_SAM_BUFF_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_BUFFERED_COUNT.3
+man/man3/BL_SAM_BUFF_BUFF_SIZE.3
+man/man3/BL_SAM_BUFF_DISCARDED_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_DISCARDED_SCORE_SUM.3
+man/man3/BL_SAM_BUFF_DISCARDED_TRAILING.3
+man/man3/BL_SAM_BUFF_MAPQ_HIGH.3
+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_COUNT.3
+man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3
+man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3
+man/man3/BL_SAM_BUFF_PREVIOUS_POS.3
+man/man3/BL_SAM_BUFF_PREVIOUS_RNAME.3
+man/man3/BL_SAM_BUFF_READS_USED.3
+man/man3/BL_SAM_BUFF_SET_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_SET_BUFFERED_COUNT.3
+man/man3/BL_SAM_BUFF_SET_BUFF_SIZE.3
+man/man3/BL_SAM_BUFF_SET_DISCARDED_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_SET_DISCARDED_SCORE_SUM.3
+man/man3/BL_SAM_BUFF_SET_DISCARDED_TRAILING.3
+man/man3/BL_SAM_BUFF_SET_MAPQ_HIGH.3
+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_COUNT.3
+man/man3/BL_SAM_BUFF_SET_MAX_DISCARDED_SCORE.3
+man/man3/BL_SAM_BUFF_SET_MIN_DISCARDED_SCORE.3
+man/man3/BL_SAM_BUFF_SET_PREVIOUS_POS.3
+man/man3/BL_SAM_BUFF_SET_PREVIOUS_RNAME.3
+man/man3/BL_SAM_BUFF_SET_READS_USED.3
+man/man3/BL_SAM_BUFF_SET_TOTAL_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_SET_TRAILING_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_SET_UNMAPPED_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_TOTAL_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3
+man/man3/BL_SAM_CIGAR.3
+man/man3/BL_SAM_FLAG.3
+man/man3/BL_SAM_MAPQ.3
+man/man3/BL_SAM_PNEXT.3
+man/man3/BL_SAM_POS.3
+man/man3/BL_SAM_QNAME.3
+man/man3/BL_SAM_QUAL.3
+man/man3/BL_SAM_QUAL_LEN.3
+man/man3/BL_SAM_RNAME.3
+man/man3/BL_SAM_RNEXT.3
+man/man3/BL_SAM_SEQ.3
+man/man3/BL_SAM_SEQ_LEN.3
+man/man3/BL_SAM_SET_CIGAR.3
+man/man3/BL_SAM_SET_FLAG.3
+man/man3/BL_SAM_SET_MAPQ.3
+man/man3/BL_SAM_SET_PNEXT.3
+man/man3/BL_SAM_SET_POS.3
+man/man3/BL_SAM_SET_QNAME.3
+man/man3/BL_SAM_SET_QUAL.3
+man/man3/BL_SAM_SET_QUAL_LEN.3
+man/man3/BL_SAM_SET_RNAME.3
+man/man3/BL_SAM_SET_RNEXT.3
+man/man3/BL_SAM_SET_SEQ.3
+man/man3/BL_SAM_SET_SEQ_LEN.3
+man/man3/BL_SAM_SET_TLEN.3
+man/man3/BL_SAM_TLEN.3
+man/man3/BL_VCF_ALT.3
+man/man3/BL_VCF_ALT_COUNT.3
+man/man3/BL_VCF_CHROMOSOME.3
+man/man3/BL_VCF_FILTER.3
+man/man3/BL_VCF_FORMAT.3
+man/man3/BL_VCF_FORMAT_MAX.3
+man/man3/BL_VCF_ID.3
+man/man3/BL_VCF_INFO.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_OTHER_COUNT.3
+man/man3/BL_VCF_PHREDS.3
+man/man3/BL_VCF_PHRED_BUFF_SIZE.3
+man/man3/BL_VCF_PHRED_COUNT.3
+man/man3/BL_VCF_POS.3
+man/man3/BL_VCF_QUALITY.3
+man/man3/BL_VCF_REF.3
+man/man3/BL_VCF_REF_COUNT.3
+man/man3/BL_VCF_SAMPLE_MAX.3
+man/man3/BL_VCF_SET_ALT.3
+man/man3/BL_VCF_SET_ALT_COUNT.3
+man/man3/BL_VCF_SET_CHROMOSOME.3
+man/man3/BL_VCF_SET_FILTER.3
+man/man3/BL_VCF_SET_FORMAT.3
+man/man3/BL_VCF_SET_FORMAT_MAX.3
+man/man3/BL_VCF_SET_ID.3
+man/man3/BL_VCF_SET_INFO.3
+man/man3/BL_VCF_SET_INFO_LEN.3
+man/man3/BL_VCF_SET_INFO_MAX.3
+man/man3/BL_VCF_SET_MULTI_SAMPLES.3
+man/man3/BL_VCF_SET_OTHER_COUNT.3
+man/man3/BL_VCF_SET_PHREDS.3
+man/man3/BL_VCF_SET_PHRED_BUFF_SIZE.3
+man/man3/BL_VCF_SET_PHRED_COUNT.3
+man/man3/BL_VCF_SET_POS.3
+man/man3/BL_VCF_SET_QUALITY.3
+man/man3/BL_VCF_SET_REF.3
+man/man3/BL_VCF_SET_REF_COUNT.3
+man/man3/BL_VCF_SET_SAMPLE_MAX.3
+man/man3/BL_VCF_SET_SINGLE_SAMPLE.3
+man/man3/BL_VCF_SINGLE_SAMPLE.3
man/man3/biolibc.3
-man/man3/chromosome_name_cmp.3
-man/man3/csv_read_field.3
-man/man3/csv_skip_field.3
-man/man3/csv_skip_rest_of_line.3
-man/man3/dsv_copy_line.3
-man/man3/dsv_free_line.3
-man/man3/dsv_read_field.3
-man/man3/dsv_read_line.3
-man/man3/dsv_skip_field.3
-man/man3/dsv_skip_rest_of_line.3
-man/man3/dsv_write_line.3
-man/man3/gff_read_feature.3
-man/man3/gff_to_bed.3
-man/man3/gff_write_feature.3
-man/man3/pos_list_add_position.3
-man/man3/pos_list_allocate.3
-man/man3/pos_list_free.3
-man/man3/pos_list_from_csv.3
-man/man3/pos_list_sort.3
-man/man3/sam_buff_add_alignment.3
-man/man3/sam_buff_alignment_ok.3
-man/man3/sam_buff_check_order.3
-man/man3/sam_buff_free_alignment.3
-man/man3/sam_buff_init.3
-man/man3/sam_buff_out_of_order.3
-man/man3/sam_buff_shift.3
-man/man3/sam_copy_alignment.3
-man/man3/sam_free_alignment.3
-man/man3/sam_init_alignment.3
-man/man3/sam_read_alignment.3
-man/man3/tsv_read_field.3
-man/man3/tsv_skip_field.3
-man/man3/tsv_skip_rest_of_line.3
-man/man3/vcf_call_downstream_of_alignment.3
-man/man3/vcf_call_free.3
-man/man3/vcf_call_in_alignment.3
-man/man3/vcf_call_init.3
-man/man3/vcf_get_sample_ids.3
-man/man3/vcf_out_of_order.3
-man/man3/vcf_parse_field_spec.3
-man/man3/vcf_read_ss_call.3
-man/man3/vcf_read_static_fields.3
-man/man3/vcf_sample_alloc.3
-man/man3/vcf_skip_header.3
-man/man3/vcf_write_ss_call.3
-man/man3/vcf_write_static_fields.3
+man/man3/bl_bed_check_order.3
+man/man3/bl_bed_gff_cmp.3
+man/man3/bl_bed_read_feature.3
+man/man3/bl_bed_skip_header.3
+man/man3/bl_bed_write_feature.3
+man/man3/bl_chromosome_name_cmp.3
+man/man3/bl_gff_read_feature.3
+man/man3/bl_gff_skip_header.3
+man/man3/bl_gff_to_bed.3
+man/man3/bl_gff_write_feature.3
+man/man3/bl_overlap_print.3
+man/man3/bl_overlap_set_all.3
+man/man3/bl_pos_list_add_position.3
+man/man3/bl_pos_list_allocate.3
+man/man3/bl_pos_list_free.3
+man/man3/bl_pos_list_from_csv.3
+man/man3/bl_pos_list_sort.3
+man/man3/bl_sam_buff_add_alignment.3
+man/man3/bl_sam_buff_alignment_ok.3
+man/man3/bl_sam_buff_check_order.3
+man/man3/bl_sam_buff_free_alignment.3
+man/man3/bl_sam_buff_init.3
+man/man3/bl_sam_buff_out_of_order.3
+man/man3/bl_sam_buff_shift.3
+man/man3/bl_sam_copy_alignment.3
+man/man3/bl_sam_free_alignment.3
+man/man3/bl_sam_init_alignment.3
+man/man3/bl_sam_read_alignment.3
+man/man3/bl_sam_write_alignment.3
+man/man3/bl_vcf_call_downstream_of_alignment.3
+man/man3/bl_vcf_call_free.3
+man/man3/bl_vcf_call_in_alignment.3
+man/man3/bl_vcf_call_init.3
+man/man3/bl_vcf_get_sample_ids.3
+man/man3/bl_vcf_out_of_order.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_skip_header.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 56a709d257..13d1e79a8d 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>=0.1.3.21
+BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.1.3.43
BUILDLINK_PKGSRCDIR.biolibc?= ../../wip/biolibc
.endif # BIOLIBC_BUILDLINK3_MK
diff --git a/biolibc/distinfo b/biolibc/distinfo
index b892a3e1e3..b46f92cf72 100644
--- a/biolibc/distinfo
+++ b/biolibc/distinfo
@@ -1,6 +1,6 @@
$NetBSD$
-SHA1 (biolibc-0.1.3.21-6b5ac39edda905980da19042afe1e3e46d92d432.tar.gz) = 084649d395f328013fcf9b46243bdfaae9e54b3d
-RMD160 (biolibc-0.1.3.21-6b5ac39edda905980da19042afe1e3e46d92d432.tar.gz) = 15ba297661d9bdfcc1f2641f4a2b4355568d4e00
-SHA512 (biolibc-0.1.3.21-6b5ac39edda905980da19042afe1e3e46d92d432.tar.gz) = 8f25d24d3ec2f2ae1fab8297e49b725324131aae8ee95ebe18e511d701ea349370d25939ae42d9174d33c4c8a70fed3217fa32c8dc2c7101c01ca5bdb468c02a
-Size (biolibc-0.1.3.21-6b5ac39edda905980da19042afe1e3e46d92d432.tar.gz) = 45009 bytes
+SHA1 (biolibc-0.1.3.43-d1d99c030d9b6b4e36b868f449e8de7d13188de8.tar.gz) = ed4bf2bcb2bea3e3a2878d0de419df4f1669cf18
+RMD160 (biolibc-0.1.3.43-d1d99c030d9b6b4e36b868f449e8de7d13188de8.tar.gz) = 9006a4555667c01e08a80c420e3bb0c7e9a6fa6b
+SHA512 (biolibc-0.1.3.43-d1d99c030d9b6b4e36b868f449e8de7d13188de8.tar.gz) = e4dce2c77ef5199f231747bba29cd77fce317480d5160c68113d36d895c7c671acc55abfde501bd051ea7ed82a2b890b8d60931b5c770f4309c131fcc7389a9e
+Size (biolibc-0.1.3.43-d1d99c030d9b6b4e36b868f449e8de7d13188de8.tar.gz) = 51198 bytes
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