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biology/biolibc: Update to 0.2.1

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Add orf.c with start/stop codon locators
Standardize BED and GFF APIs
Implement VCF input filtering
Eliminate mutator macros mirroring mutator functions
Numerous minor bug fixes and enhancements

Changes: https://github.com/auerlab/biolibc/releases/tag/0.2.1
This commit is contained in:
Jason W. Bacon 2021-12-14 13:40:13 -06:00
parent 14e134a37b
commit 0646ba904f
3 changed files with 8 additions and 183 deletions
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3
biology/biolibc/Makefile
View File

@ -1,6 +1,5 @@
PORTNAME= biolibc
DISTVERSION= 0.2.0-11
DISTVERSIONSUFFIX= -g65b3b13
DISTVERSION= 0.2.1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org

6
biology/biolibc/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1631891740
SHA256 (auerlab-biolibc-0.2.0-11-g65b3b13_GH0.tar.gz) = e4efb3e081c0a48d815e2e5e23ce4c6f1d758e222d735fa9719e588a8dc04318
SIZE (auerlab-biolibc-0.2.0-11-g65b3b13_GH0.tar.gz) = 119311
TIMESTAMP = 1639331819
SHA256 (auerlab-biolibc-0.2.1_GH0.tar.gz) = c3a3ac20c549a7a7626c77bdb86e81bc01ece864c2818a1fa744614e81f9eda3
SIZE (auerlab-biolibc-0.2.1_GH0.tar.gz) = 104282

182
biology/biolibc/pkg-plist
View File

@ -9,6 +9,7 @@ include/biolibc/overlap.h
include/biolibc/pos-list.h
include/biolibc/sam-buff.h
include/biolibc/sam.h
include/biolibc/translate.h
include/biolibc/vcf.h
lib/libbiolibc.a
lib/libbiolibc.so
@ -29,29 +30,6 @@ man/man3/BL_BED_ITEM_RGB_AE.3.gz
man/man3/BL_BED_NAME.3.gz
man/man3/BL_BED_NAME_AE.3.gz
man/man3/BL_BED_SCORE.3.gz
man/man3/BL_BED_SET_BLOCK_COUNT.3.gz
man/man3/BL_BED_SET_BLOCK_SIZES.3.gz
man/man3/BL_BED_SET_BLOCK_SIZES_AE.3.gz
man/man3/BL_BED_SET_BLOCK_SIZES_CPY.3.gz
man/man3/BL_BED_SET_BLOCK_STARTS.3.gz
man/man3/BL_BED_SET_BLOCK_STARTS_AE.3.gz
man/man3/BL_BED_SET_BLOCK_STARTS_CPY.3.gz
man/man3/BL_BED_SET_CHROM.3.gz
man/man3/BL_BED_SET_CHROM_AE.3.gz
man/man3/BL_BED_SET_CHROM_CPY.3.gz
man/man3/BL_BED_SET_CHROM_END.3.gz
man/man3/BL_BED_SET_CHROM_START.3.gz
man/man3/BL_BED_SET_FIELDS.3.gz
man/man3/BL_BED_SET_ITEM_RGB.3.gz
man/man3/BL_BED_SET_ITEM_RGB_AE.3.gz
man/man3/BL_BED_SET_ITEM_RGB_CPY.3.gz
man/man3/BL_BED_SET_NAME.3.gz
man/man3/BL_BED_SET_NAME_AE.3.gz
man/man3/BL_BED_SET_NAME_CPY.3.gz
man/man3/BL_BED_SET_SCORE.3.gz
man/man3/BL_BED_SET_STRAND.3.gz
man/man3/BL_BED_SET_THICK_END.3.gz
man/man3/BL_BED_SET_THICK_START.3.gz
man/man3/BL_BED_STRAND.3.gz
man/man3/BL_BED_THICK_END.3.gz
man/man3/BL_BED_THICK_START.3.gz
@ -63,16 +41,6 @@ man/man3/BL_FASTA_SEQ.3.gz
man/man3/BL_FASTA_SEQ_AE.3.gz
man/man3/BL_FASTA_SEQ_ARRAY_SIZE.3.gz
man/man3/BL_FASTA_SEQ_LEN.3.gz
man/man3/BL_FASTA_SET_DESC.3.gz
man/man3/BL_FASTA_SET_DESC_AE.3.gz
man/man3/BL_FASTA_SET_DESC_ARRAY_SIZE.3.gz
man/man3/BL_FASTA_SET_DESC_CPY.3.gz
man/man3/BL_FASTA_SET_DESC_LEN.3.gz
man/man3/BL_FASTA_SET_SEQ.3.gz
man/man3/BL_FASTA_SET_SEQ_AE.3.gz
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_FASTQ_DESC.3.gz
man/man3/BL_FASTQ_DESC_AE.3.gz
man/man3/BL_FASTQ_DESC_ARRAY_SIZE.3.gz
@ -89,26 +57,6 @@ 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_FASTQ_SET_DESC.3.gz
man/man3/BL_FASTQ_SET_DESC_AE.3.gz
man/man3/BL_FASTQ_SET_DESC_ARRAY_SIZE.3.gz
man/man3/BL_FASTQ_SET_DESC_CPY.3.gz
man/man3/BL_FASTQ_SET_DESC_LEN.3.gz
man/man3/BL_FASTQ_SET_PLUS.3.gz
man/man3/BL_FASTQ_SET_PLUS_AE.3.gz
man/man3/BL_FASTQ_SET_PLUS_ARRAY_SIZE.3.gz
man/man3/BL_FASTQ_SET_PLUS_CPY.3.gz
man/man3/BL_FASTQ_SET_PLUS_LEN.3.gz
man/man3/BL_FASTQ_SET_QUAL.3.gz
man/man3/BL_FASTQ_SET_QUAL_AE.3.gz
man/man3/BL_FASTQ_SET_QUAL_ARRAY_SIZE.3.gz
man/man3/BL_FASTQ_SET_QUAL_CPY.3.gz
man/man3/BL_FASTQ_SET_QUAL_LEN.3.gz
man/man3/BL_FASTQ_SET_SEQ.3.gz
man/man3/BL_FASTQ_SET_SEQ_AE.3.gz
man/man3/BL_FASTQ_SET_SEQ_ARRAY_SIZE.3.gz
man/man3/BL_FASTQ_SET_SEQ_CPY.3.gz
man/man3/BL_FASTQ_SET_SEQ_LEN.3.gz
man/man3/BL_GFF_ATTRIBUTES.3.gz
man/man3/BL_GFF_ATTRIBUTES_AE.3.gz
man/man3/BL_GFF_END.3.gz
@ -122,29 +70,6 @@ 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_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.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_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.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_SOURCE.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_SOURCE.3.gz
man/man3/BL_GFF_SOURCE_AE.3.gz
man/man3/BL_GFF_START.3.gz
@ -154,20 +79,10 @@ man/man3/BL_OVERLAP_FEATURE2_LEN.3.gz
man/man3/BL_OVERLAP_OVERLAP_END.3.gz
man/man3/BL_OVERLAP_OVERLAP_LEN.3.gz
man/man3/BL_OVERLAP_OVERLAP_START.3.gz
man/man3/BL_OVERLAP_SET_FEATURE1_LEN.3.gz
man/man3/BL_OVERLAP_SET_FEATURE2_LEN.3.gz
man/man3/BL_OVERLAP_SET_OVERLAP_END.3.gz
man/man3/BL_OVERLAP_SET_OVERLAP_LEN.3.gz
man/man3/BL_OVERLAP_SET_OVERLAP_START.3.gz
man/man3/BL_POS_LIST_ARRAY_SIZE.3.gz
man/man3/BL_POS_LIST_COUNT.3.gz
man/man3/BL_POS_LIST_POSITIONS.3.gz
man/man3/BL_POS_LIST_POSITIONS_AE.3.gz
man/man3/BL_POS_LIST_SET_ARRAY_SIZE.3.gz
man/man3/BL_POS_LIST_SET_COUNT.3.gz
man/man3/BL_POS_LIST_SET_POSITIONS.3.gz
man/man3/BL_POS_LIST_SET_POSITIONS_AE.3.gz
man/man3/BL_POS_LIST_SET_POSITIONS_CPY.3.gz
man/man3/BL_SAM_BUFF_ALIGNMENTS.3.gz
man/man3/BL_SAM_BUFF_ALIGNMENTS_AE.3.gz
man/man3/BL_SAM_BUFF_BUFFERED_COUNT.3.gz
@ -189,29 +104,6 @@ man/man3/BL_SAM_BUFF_PREVIOUS_POS.3.gz
man/man3/BL_SAM_BUFF_PREVIOUS_RNAME.3.gz
man/man3/BL_SAM_BUFF_PREVIOUS_RNAME_AE.3.gz
man/man3/BL_SAM_BUFF_READS_USED.3.gz
man/man3/BL_SAM_BUFF_SET_ALIGNMENTS.3.gz
man/man3/BL_SAM_BUFF_SET_ALIGNMENTS_AE.3.gz
man/man3/BL_SAM_BUFF_SET_ALIGNMENTS_CPY.3.gz
man/man3/BL_SAM_BUFF_SET_BUFFERED_COUNT.3.gz
man/man3/BL_SAM_BUFF_SET_BUFF_SIZE.3.gz
man/man3/BL_SAM_BUFF_SET_DISCARDED_ALIGNMENTS.3.gz
man/man3/BL_SAM_BUFF_SET_DISCARDED_SCORE_SUM.3.gz
man/man3/BL_SAM_BUFF_SET_DISCARDED_TRAILING.3.gz
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_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
man/man3/BL_SAM_BUFF_SET_PREVIOUS_POS.3.gz
man/man3/BL_SAM_BUFF_SET_PREVIOUS_RNAME.3.gz
man/man3/BL_SAM_BUFF_SET_PREVIOUS_RNAME_AE.3.gz
man/man3/BL_SAM_BUFF_SET_PREVIOUS_RNAME_CPY.3.gz
man/man3/BL_SAM_BUFF_SET_READS_USED.3.gz
man/man3/BL_SAM_BUFF_SET_TOTAL_ALIGNMENTS.3.gz
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_TOTAL_ALIGNMENTS.3.gz
man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3.gz
man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3.gz
@ -233,31 +125,6 @@ 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_LEN.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_CPY.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
man/man3/BL_SAM_SET_POS.3.gz
man/man3/BL_SAM_SET_QNAME.3.gz
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_CPY.3.gz
man/man3/BL_SAM_SET_QUAL_LEN.3.gz
man/man3/BL_SAM_SET_RNAME.3.gz
man/man3/BL_SAM_SET_RNAME_AE.3.gz
man/man3/BL_SAM_SET_RNAME_CPY.3.gz
man/man3/BL_SAM_SET_RNEXT.3.gz
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_CPY.3.gz
man/man3/BL_SAM_SET_SEQ_LEN.3.gz
man/man3/BL_SAM_SET_TLEN.3.gz
man/man3/BL_SAM_TLEN.3.gz
man/man3/BL_VCF_ALT.3.gz
man/man3/BL_VCF_ALT_AE.3.gz
@ -289,49 +156,6 @@ 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_MAX.3.gz
man/man3/BL_VCF_SET_ALT.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
man/man3/BL_VCF_SET_CHROM.3.gz
man/man3/BL_VCF_SET_CHROM_AE.3.gz
man/man3/BL_VCF_SET_CHROM_CPY.3.gz
man/man3/BL_VCF_SET_FILTER.3.gz
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_CPY.3.gz
man/man3/BL_VCF_SET_FORMAT_MAX.3.gz
man/man3/BL_VCF_SET_ID.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_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_SAMPLES.3.gz
man/man3/BL_VCF_SET_MULTI_SAMPLES_AE.3.gz
man/man3/BL_VCF_SET_MULTI_SAMPLES_CPY.3.gz
man/man3/BL_VCF_SET_OTHER_COUNT.3.gz
man/man3/BL_VCF_SET_PHREDS.3.gz
man/man3/BL_VCF_SET_PHREDS_AE.3.gz
man/man3/BL_VCF_SET_PHREDS_CPY.3.gz
man/man3/BL_VCF_SET_PHRED_BUFF_SIZE.3.gz
man/man3/BL_VCF_SET_PHRED_COUNT.3.gz
man/man3/BL_VCF_SET_POS.3.gz
man/man3/BL_VCF_SET_QUAL.3.gz
man/man3/BL_VCF_SET_QUAL_AE.3.gz
man/man3/BL_VCF_SET_QUAL_CPY.3.gz
man/man3/BL_VCF_SET_REF.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_CPY.3.gz
man/man3/BL_VCF_SINGLE_SAMPLE.3.gz
man/man3/BL_VCF_SINGLE_SAMPLE_AE.3.gz
man/man3/biolibc.3.gz
@ -435,6 +259,8 @@ man/man3/bl_gff_set_strand.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
man/man3/bl_next_start_codon.3.gz
man/man3/bl_next_stop_codon.3.gz
man/man3/bl_overlap_print.3.gz
man/man3/bl_overlap_set_all.3.gz
man/man3/bl_overlap_set_feature1_len.3.gz
@ -554,6 +380,6 @@ 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_cpy.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