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biolibc: Update to 0.1.3.54
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Fri Jul 23 11:26:06 2021 -0500
Changeset: 0a1e18f1eee778d26a4014e7dcea7bd5c61e379f
Modified Files:
biolibc/Makefile
biolibc/PLIST
biolibc/buildlink3.mk
biolibc/distinfo
Log Message:
biolibc: Update to 0.1.3.54
Finish regenerating improved accessors and mutators
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=0a1e18f1eee778d26a4014e7dcea7bd5c61e379f
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 | 168 ++++++++++++++++++++++++++++++++++++++++++++++++++
biolibc/buildlink3.mk | 2 +-
biolibc/distinfo | 8 +--
4 files changed, 175 insertions(+), 7 deletions(-)
diffs:
diff --git a/biolibc/Makefile b/biolibc/Makefile
index 0537dcd359..fb8f1810af 100644
--- a/biolibc/Makefile
+++ b/biolibc/Makefile
@@ -1,9 +1,9 @@
# $NetBSD$
-DISTNAME= biolibc-0.1.3.50
+DISTNAME= biolibc-0.1.3.54
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG= 1f6c6845b71c82eb2a97b1b5ffa079827bcad14f
+GITHUB_TAG= 401a2dddb6aa7fb8cf2f4eadcb0df78283dd94df
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://github.com/auerlab/biolibc
diff --git a/biolibc/PLIST b/biolibc/PLIST
index b1ff2db38e..bd03821f77 100644
--- a/biolibc/PLIST
+++ b/biolibc/PLIST
@@ -14,7 +14,9 @@ lib/libbiolibc.so.2
lib/libbiolibc.so.2.0
man/man3/BL_BED_BLOCK_COUNT.3
man/man3/BL_BED_BLOCK_SIZES.3
+man/man3/BL_BED_BLOCK_SIZES_AE.3
man/man3/BL_BED_BLOCK_STARTS.3
+man/man3/BL_BED_BLOCK_STARTS_AE.3
man/man3/BL_BED_CHROM.3
man/man3/BL_BED_CHROM_AE.3
man/man3/BL_BED_CHROM_END.3
@@ -52,25 +54,43 @@ man/man3/BL_BED_STRAND.3
man/man3/BL_BED_THICK_END.3
man/man3/BL_BED_THICK_START.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_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_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.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_GENE_NAME_CPY.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_SEQUENCE_AE.3
+man/man3/BL_GFF_SET_SEQUENCE_CPY.3
man/man3/BL_GFF_SET_SOURCE.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_SOURCE.3
+man/man3/BL_GFF_SOURCE_AE.3
man/man3/BL_GFF_START.3
man/man3/BL_GFF_STRAND.3
man/man3/BL_OVERLAP_FEATURE1_LEN.3
@@ -86,10 +106,14 @@ 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_POSITIONS_AE.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_POS_LIST_SET_POSITIONS_AE.3
+man/man3/BL_POS_LIST_SET_POSITIONS_CPY.3
man/man3/BL_SAM_BUFF_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_ALIGNMENTS_AE.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
@@ -107,8 +131,11 @@ 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_PREVIOUS_RNAME_AE.3
man/man3/BL_SAM_BUFF_READS_USED.3
man/man3/BL_SAM_BUFF_SET_ALIGNMENTS.3
+man/man3/BL_SAM_BUFF_SET_ALIGNMENTS_AE.3
+man/man3/BL_SAM_BUFF_SET_ALIGNMENTS_CPY.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
@@ -123,6 +150,8 @@ 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_PREVIOUS_RNAME_AE.3
+man/man3/BL_SAM_BUFF_SET_PREVIOUS_RNAME_CPY.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
@@ -131,73 +160,124 @@ 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_CIGAR_AE.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_QNAME_AE.3
man/man3/BL_SAM_QUAL.3
+man/man3/BL_SAM_QUAL_AE.3
man/man3/BL_SAM_QUAL_LEN.3
man/man3/BL_SAM_RNAME.3
+man/man3/BL_SAM_RNAME_AE.3
man/man3/BL_SAM_RNEXT.3
+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_LEN.3
man/man3/BL_SAM_SET_CIGAR.3
+man/man3/BL_SAM_SET_CIGAR_AE.3
+man/man3/BL_SAM_SET_CIGAR_CPY.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_QNAME_AE.3
+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_CPY.3
man/man3/BL_SAM_SET_QUAL_LEN.3
man/man3/BL_SAM_SET_RNAME.3
+man/man3/BL_SAM_SET_RNAME_AE.3
+man/man3/BL_SAM_SET_RNAME_CPY.3
man/man3/BL_SAM_SET_RNEXT.3
+man/man3/BL_SAM_SET_RNEXT_AE.3
+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_CPY.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_AE.3
man/man3/BL_VCF_ALT_COUNT.3
man/man3/BL_VCF_CHROM.3
+man/man3/BL_VCF_CHROM_AE.3
man/man3/BL_VCF_FILTER.3
+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_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_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_OTHER_COUNT.3
man/man3/BL_VCF_PHREDS.3
+man/man3/BL_VCF_PHREDS_AE.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_QUAL.3
+man/man3/BL_VCF_QUAL_AE.3
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_MAX.3
man/man3/BL_VCF_SET_ALT.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
man/man3/BL_VCF_SET_CHROM.3
+man/man3/BL_VCF_SET_CHROM_AE.3
+man/man3/BL_VCF_SET_CHROM_CPY.3
man/man3/BL_VCF_SET_FILTER.3
+man/man3/BL_VCF_SET_FILTER_AE.3
+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_CPY.3
man/man3/BL_VCF_SET_FORMAT_MAX.3
man/man3/BL_VCF_SET_ID.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_CPY.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_MULTI_SAMPLES_AE.3
+man/man3/BL_VCF_SET_MULTI_SAMPLES_CPY.3
man/man3/BL_VCF_SET_OTHER_COUNT.3
man/man3/BL_VCF_SET_PHREDS.3
+man/man3/BL_VCF_SET_PHREDS_AE.3
+man/man3/BL_VCF_SET_PHREDS_CPY.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_QUAL.3
+man/man3/BL_VCF_SET_QUAL_AE.3
+man/man3/BL_VCF_SET_QUAL_CPY.3
man/man3/BL_VCF_SET_REF.3
+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_CPY.3
man/man3/BL_VCF_SINGLE_SAMPLE.3
+man/man3/BL_VCF_SINGLE_SAMPLE_AE.3
man/man3/biolibc.3
man/man3/bl_bed_check_order.3
man/man3/bl_bed_gff_cmp.3
@@ -226,15 +306,45 @@ man/man3/bl_bed_skip_header.3
man/man3/bl_bed_write.3
man/man3/bl_chrom_name_cmp.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_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_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_skip_header.3
man/man3/bl_gff_to_bed.3
man/man3/bl_gff_write.3
man/man3/bl_overlap_print.3
man/man3/bl_overlap_set_all.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_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_set_array_size.3
+man/man3/bl_pos_list_set_count.3
+man/man3/bl_pos_list_set_positions.3
+man/man3/bl_pos_list_set_positions_ae.3
+man/man3/bl_pos_list_set_positions_cpy.3
man/man3/bl_pos_list_sort.3
man/man3/bl_sam_buff_add_alignment.3
man/man3/bl_sam_buff_alignment_ok.3
@@ -247,6 +357,27 @@ man/man3/bl_sam_copy.3
man/man3/bl_sam_free.3
man/man3/bl_sam_init.3
man/man3/bl_sam_read.3
+man/man3/bl_sam_set_cigar_ae.3
+man/man3/bl_sam_set_cigar_cpy.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_ae.3
+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_cpy.3
+man/man3/bl_sam_set_qual_len.3
+man/man3/bl_sam_set_rname_ae.3
+man/man3/bl_sam_set_rname_cpy.3
+man/man3/bl_sam_set_rnext_ae.3
+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_cpy.3
+man/man3/bl_sam_set_seq_len.3
+man/man3/bl_sam_set_tlen.3
man/man3/bl_sam_write.3
man/man3/bl_vcf_call_downstream_of_alignment.3
man/man3/bl_vcf_call_in_alignment.3
@@ -258,6 +389,43 @@ 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
+man/man3/bl_vcf_set_chrom_ae.3
+man/man3/bl_vcf_set_chrom_cpy.3
+man/man3/bl_vcf_set_filter_ae.3
+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_cpy.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_cpy.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_multi_samples_ae.3
+man/man3/bl_vcf_set_multi_samples_cpy.3
+man/man3/bl_vcf_set_other_count.3
+man/man3/bl_vcf_set_phred_buff_size.3
+man/man3/bl_vcf_set_phred_count.3
+man/man3/bl_vcf_set_phreds.3
+man/man3/bl_vcf_set_phreds_ae.3
+man/man3/bl_vcf_set_phreds_cpy.3
+man/man3/bl_vcf_set_pos.3
+man/man3/bl_vcf_set_qual_ae.3
+man/man3/bl_vcf_set_qual_cpy.3
+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_cpy.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 f37299ca0f..f3041c6909 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>=0.1.3.50
+BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.1.3.54
BUILDLINK_PKGSRCDIR.biolibc?= ../../wip/biolibc
.endif # BIOLIBC_BUILDLINK3_MK
diff --git a/biolibc/distinfo b/biolibc/distinfo
index 4b0ba862ba..19028bb63e 100644
--- a/biolibc/distinfo
+++ b/biolibc/distinfo
@@ -1,6 +1,6 @@
$NetBSD$
-SHA1 (biolibc-0.1.3.50-1f6c6845b71c82eb2a97b1b5ffa079827bcad14f.tar.gz) = e2b6f0c46d834861a934e315b0a1baf56adcd769
-RMD160 (biolibc-0.1.3.50-1f6c6845b71c82eb2a97b1b5ffa079827bcad14f.tar.gz) = 3ea32a85e3774dcd51a13c236bf253ec150bee08
-SHA512 (biolibc-0.1.3.50-1f6c6845b71c82eb2a97b1b5ffa079827bcad14f.tar.gz) = 68d414cd37a8f050f89f27d92528d18af6316fa5a305e9d07f2ea14e4b2cb19dd226bb7c1dc1b14ebc2998510be3f7f44fdcdfce024702dd550f14dd1797248b
-Size (biolibc-0.1.3.50-1f6c6845b71c82eb2a97b1b5ffa079827bcad14f.tar.gz) = 58755 bytes
+SHA1 (biolibc-0.1.3.54-401a2dddb6aa7fb8cf2f4eadcb0df78283dd94df.tar.gz) = 73a3fe1f237cdd9bb5a8e8d14dd0c5d80307e02e
+RMD160 (biolibc-0.1.3.54-401a2dddb6aa7fb8cf2f4eadcb0df78283dd94df.tar.gz) = f6f0e006911d1773c8d3b46dad6ec5a49e870f4f
+SHA512 (biolibc-0.1.3.54-401a2dddb6aa7fb8cf2f4eadcb0df78283dd94df.tar.gz) = d818ecf03539992d074e5efdb0e291a9bd754c70a9b1d3d8d3ce7fc8978faba0499bb5da036ebf4c5de518bcbdb79318fb579c9704b8332dfdf63ec4abecab13
+Size (biolibc-0.1.3.54-401a2dddb6aa7fb8cf2f4eadcb0df78283dd94df.tar.gz) = 91717 bytes
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