Tue Mar 15 21:06:32 2022 UTC ()
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


(bacon)
diff -r1.7 -r1.8 pkgsrc/biology/biolibc/Makefile
diff -r1.7 -r1.8 pkgsrc/biology/biolibc/PLIST
diff -r1.7 -r1.8 pkgsrc/biology/biolibc/buildlink3.mk
diff -r1.9 -r1.10 pkgsrc/biology/biolibc/distinfo
cvs diff -r1.7 -r1.8 pkgsrc/biology/biolibc/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/biolibc/Makefile 2021/12/14 18:58:56 1.7
+++ pkgsrc/biology/biolibc/Makefile 2022/03/15 21:06:32 1.8
@@ -1,16 +1,16 @@ @@ -1,16 +1,16 @@
1# $NetBSD: Makefile,v 1.7 2021/12/14 18:58:56 bacon Exp $ 1# $NetBSD: Makefile,v 1.8 2022/03/15 21:06:32 bacon Exp $
2 2
3DISTNAME= biolibc-0.2.1 3DISTNAME= biolibc-0.2.2
4CATEGORIES= biology 4CATEGORIES= biology
5MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/} 5MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/}
6 6
7MAINTAINER= bacon@NetBSD.org 7MAINTAINER= bacon@NetBSD.org
8HOMEPAGE= https://github.com/auerlab/biolibc 8HOMEPAGE= https://github.com/auerlab/biolibc
9COMMENT= Low-level high-performance bioinformatics library 9COMMENT= Low-level high-performance bioinformatics library
10LICENSE= 2-clause-bsd 10LICENSE= 2-clause-bsd
11 11
12.include "../../mk/bsd.prefs.mk" 12.include "../../mk/bsd.prefs.mk"
13 13
14.if ${OPSYS} == Darwin 14.if ${OPSYS} == Darwin
15BUILD_TARGET= apple 15BUILD_TARGET= apple
16INSTALL_TARGET= apple-install 16INSTALL_TARGET= apple-install
cvs diff -r1.7 -r1.8 pkgsrc/biology/biolibc/PLIST (expand / switch to unified diff)

--- pkgsrc/biology/biolibc/PLIST 2021/12/14 18:58:56 1.7
+++ pkgsrc/biology/biolibc/PLIST 2022/03/15 21:06:32 1.8
@@ -1,31 +1,71 @@ @@ -1,31 +1,71 @@
1@comment $NetBSD: PLIST,v 1.7 2021/12/14 18:58:56 bacon Exp $ 1@comment $NetBSD: PLIST,v 1.8 2022/03/15 21:06:32 bacon Exp $
 2include/biolibc/align-accessors.h
 3include/biolibc/align-mutators.h
 4include/biolibc/align-rvs.h
 5include/biolibc/align.h
 6include/biolibc/bed-accessors.h
 7include/biolibc/bed-mutators.h
 8include/biolibc/bed-rvs.h
2include/biolibc/bed.h 9include/biolibc/bed.h
3include/biolibc/biolibc.h 10include/biolibc/biolibc.h
4include/biolibc/biostring.h 11include/biolibc/biostring.h
 12include/biolibc/fasta-accessors.h
 13include/biolibc/fasta-mutators.h
 14include/biolibc/fasta-rvs.h
5include/biolibc/fasta.h 15include/biolibc/fasta.h
 16include/biolibc/fastq-accessors.h
 17include/biolibc/fastq-mutators.h
 18include/biolibc/fastq-rvs.h
6include/biolibc/fastq.h 19include/biolibc/fastq.h
 20include/biolibc/fastx-accessors.h
 21include/biolibc/fastx-mutators.h
 22include/biolibc/fastx-rvs.h
7include/biolibc/fastx.h 23include/biolibc/fastx.h
 24include/biolibc/gff-accessors.h
 25include/biolibc/gff-index-accessors.h
 26include/biolibc/gff-index-mutators.h
 27include/biolibc/gff-index-rvs.h
 28include/biolibc/gff-index.h
 29include/biolibc/gff-mutators.h
 30include/biolibc/gff-rvs.h
8include/biolibc/gff.h 31include/biolibc/gff.h
 32include/biolibc/overlap-accessors.h
 33include/biolibc/overlap-mutators.h
 34include/biolibc/overlap-rvs.h
9include/biolibc/overlap.h 35include/biolibc/overlap.h
 36include/biolibc/pos-list-accessors.h
 37include/biolibc/pos-list-mutators.h
 38include/biolibc/pos-list-rvs.h
10include/biolibc/pos-list.h 39include/biolibc/pos-list.h
 40include/biolibc/sam-accessors.h
 41include/biolibc/sam-buff-accessors.h
 42include/biolibc/sam-buff-mutators.h
 43include/biolibc/sam-buff-rvs.h
11include/biolibc/sam-buff.h 44include/biolibc/sam-buff.h
 45include/biolibc/sam-mutators.h
 46include/biolibc/sam-rvs.h
12include/biolibc/sam.h 47include/biolibc/sam.h
13include/biolibc/translate.h 48include/biolibc/translate.h
 49include/biolibc/vcf-accessors.h
 50include/biolibc/vcf-mutators.h
 51include/biolibc/vcf-rvs.h
14include/biolibc/vcf.h 52include/biolibc/vcf.h
15lib/libbiolibc.a 53lib/libbiolibc.a
16lib/libbiolibc.so 54lib/libbiolibc.so
17lib/libbiolibc.so.2 55lib/libbiolibc.so.2
18lib/libbiolibc.so.2.0 56lib/libbiolibc.so.2.0
 57man/man3/BL_ALIGN_MAX_MISMATCH_PERCENT.3
 58man/man3/BL_ALIGN_MIN_MATCH.3
19man/man3/BL_BED_BLOCK_COUNT.3 59man/man3/BL_BED_BLOCK_COUNT.3
20man/man3/BL_BED_BLOCK_SIZES.3 60man/man3/BL_BED_BLOCK_SIZES.3
21man/man3/BL_BED_BLOCK_SIZES_AE.3 61man/man3/BL_BED_BLOCK_SIZES_AE.3
22man/man3/BL_BED_BLOCK_STARTS.3 62man/man3/BL_BED_BLOCK_STARTS.3
23man/man3/BL_BED_BLOCK_STARTS_AE.3 63man/man3/BL_BED_BLOCK_STARTS_AE.3
24man/man3/BL_BED_CHROM.3 64man/man3/BL_BED_CHROM.3
25man/man3/BL_BED_CHROM_AE.3 65man/man3/BL_BED_CHROM_AE.3
26man/man3/BL_BED_CHROM_END.3 66man/man3/BL_BED_CHROM_END.3
27man/man3/BL_BED_CHROM_START.3 67man/man3/BL_BED_CHROM_START.3
28man/man3/BL_BED_FIELDS.3 68man/man3/BL_BED_FIELDS.3
29man/man3/BL_BED_ITEM_RGB.3 69man/man3/BL_BED_ITEM_RGB.3
30man/man3/BL_BED_ITEM_RGB_AE.3 70man/man3/BL_BED_ITEM_RGB_AE.3
31man/man3/BL_BED_NAME.3 71man/man3/BL_BED_NAME.3
@@ -48,66 +88,83 @@ man/man3/BL_FASTQ_DESC_ARRAY_SIZE.3 @@ -48,66 +88,83 @@ man/man3/BL_FASTQ_DESC_ARRAY_SIZE.3
48man/man3/BL_FASTQ_DESC_LEN.3 88man/man3/BL_FASTQ_DESC_LEN.3
49man/man3/BL_FASTQ_PLUS.3 89man/man3/BL_FASTQ_PLUS.3
50man/man3/BL_FASTQ_PLUS_AE.3 90man/man3/BL_FASTQ_PLUS_AE.3
51man/man3/BL_FASTQ_PLUS_ARRAY_SIZE.3 91man/man3/BL_FASTQ_PLUS_ARRAY_SIZE.3
52man/man3/BL_FASTQ_PLUS_LEN.3 92man/man3/BL_FASTQ_PLUS_LEN.3
53man/man3/BL_FASTQ_QUAL.3 93man/man3/BL_FASTQ_QUAL.3
54man/man3/BL_FASTQ_QUAL_AE.3 94man/man3/BL_FASTQ_QUAL_AE.3
55man/man3/BL_FASTQ_QUAL_ARRAY_SIZE.3 95man/man3/BL_FASTQ_QUAL_ARRAY_SIZE.3
56man/man3/BL_FASTQ_QUAL_LEN.3 96man/man3/BL_FASTQ_QUAL_LEN.3
57man/man3/BL_FASTQ_SEQ.3 97man/man3/BL_FASTQ_SEQ.3
58man/man3/BL_FASTQ_SEQ_AE.3 98man/man3/BL_FASTQ_SEQ_AE.3
59man/man3/BL_FASTQ_SEQ_ARRAY_SIZE.3 99man/man3/BL_FASTQ_SEQ_ARRAY_SIZE.3
60man/man3/BL_FASTQ_SEQ_LEN.3 100man/man3/BL_FASTQ_SEQ_LEN.3
 101man/man3/BL_FASTX_FASTA.3
 102man/man3/BL_FASTX_FASTQ.3
 103man/man3/BL_FASTX_FORMAT.3
 104man/man3/BL_FASTX_UNION.3
 105man/man3/BL_FASTX_}.3
61man/man3/BL_GFF_ATTRIBUTES.3 106man/man3/BL_GFF_ATTRIBUTES.3
62man/man3/BL_GFF_ATTRIBUTES_AE.3 107man/man3/BL_GFF_ATTRIBUTES_AE.3
63man/man3/BL_GFF_END.3 108man/man3/BL_GFF_END.3
64man/man3/BL_GFF_FEATURE.3 
65man/man3/BL_GFF_FEATURE_AE.3 
66man/man3/BL_GFF_FEATURE_ID.3 109man/man3/BL_GFF_FEATURE_ID.3
67man/man3/BL_GFF_FEATURE_ID_AE.3 110man/man3/BL_GFF_FEATURE_ID_AE.3
68man/man3/BL_GFF_GENE_NAME.3 111man/man3/BL_GFF_FEATURE_NAME.3
69man/man3/BL_GFF_GENE_NAME_AE.3 112man/man3/BL_GFF_FEATURE_NAME_AE.3
 113man/man3/BL_GFF_FILE_POS.3
 114man/man3/BL_GFF_INDEX_ARRAY_SIZE.3
 115man/man3/BL_GFF_INDEX_COUNT.3
 116man/man3/BL_GFF_INDEX_END.3
 117man/man3/BL_GFF_INDEX_END_AE.3
 118man/man3/BL_GFF_INDEX_FILE_POS.3
 119man/man3/BL_GFF_INDEX_FILE_POS_AE.3
 120man/man3/BL_GFF_INDEX_SEQID.3
 121man/man3/BL_GFF_INDEX_SEQID_AE.3
 122man/man3/BL_GFF_INDEX_START.3
 123man/man3/BL_GFF_INDEX_START_AE.3
70man/man3/BL_GFF_PHASE.3 124man/man3/BL_GFF_PHASE.3
71man/man3/BL_GFF_SCORE.3 125man/man3/BL_GFF_SCORE.3
72man/man3/BL_GFF_SEQUENCE.3 126man/man3/BL_GFF_SEQID.3
73man/man3/BL_GFF_SEQUENCE_AE.3 127man/man3/BL_GFF_SEQID_AE.3
74man/man3/BL_GFF_SOURCE.3 128man/man3/BL_GFF_SOURCE.3
75man/man3/BL_GFF_SOURCE_AE.3 129man/man3/BL_GFF_SOURCE_AE.3
76man/man3/BL_GFF_START.3 130man/man3/BL_GFF_START.3
77man/man3/BL_GFF_STRAND.3 131man/man3/BL_GFF_STRAND.3
 132man/man3/BL_GFF_TYPE.3
 133man/man3/BL_GFF_TYPE_AE.3
78man/man3/BL_OVERLAP_FEATURE1_LEN.3 134man/man3/BL_OVERLAP_FEATURE1_LEN.3
79man/man3/BL_OVERLAP_FEATURE2_LEN.3 135man/man3/BL_OVERLAP_FEATURE2_LEN.3
80man/man3/BL_OVERLAP_OVERLAP_END.3 136man/man3/BL_OVERLAP_OVERLAP_END.3
81man/man3/BL_OVERLAP_OVERLAP_LEN.3 137man/man3/BL_OVERLAP_OVERLAP_LEN.3
82man/man3/BL_OVERLAP_OVERLAP_START.3 138man/man3/BL_OVERLAP_OVERLAP_START.3
83man/man3/BL_POS_LIST_ARRAY_SIZE.3 139man/man3/BL_POS_LIST_ARRAY_SIZE.3
84man/man3/BL_POS_LIST_COUNT.3 140man/man3/BL_POS_LIST_COUNT.3
85man/man3/BL_POS_LIST_POSITIONS.3 141man/man3/BL_POS_LIST_POSITIONS.3
86man/man3/BL_POS_LIST_POSITIONS_AE.3 142man/man3/BL_POS_LIST_POSITIONS_AE.3
87man/man3/BL_SAM_BUFF_ALIGNMENTS.3 143man/man3/BL_SAM_BUFF_ALIGNMENTS.3
88man/man3/BL_SAM_BUFF_ALIGNMENTS_AE.3 144man/man3/BL_SAM_BUFF_ALIGNMENTS_AE.3
89man/man3/BL_SAM_BUFF_BUFFERED_COUNT.3 145man/man3/BL_SAM_BUFF_BUFFERED_COUNT.3
90man/man3/BL_SAM_BUFF_BUFF_SIZE.3 146man/man3/BL_SAM_BUFF_BUFF_SIZE.3
91man/man3/BL_SAM_BUFF_DISCARDED_ALIGNMENTS.3 147man/man3/BL_SAM_BUFF_DISCARDED_ALIGNMENTS.3
92man/man3/BL_SAM_BUFF_DISCARDED_SCORE_SUM.3 148man/man3/BL_SAM_BUFF_DISCARDED_SCORE_SUM.3
93man/man3/BL_SAM_BUFF_DISCARDED_TRAILING.3 149man/man3/BL_SAM_BUFF_DISCARDED_TRAILING.3
94man/man3/BL_SAM_BUFF_INC_DISCARDED_TRAILING.3 150man/man3/BL_SAM_BUFF_INC_DISCARDED_TRAILING.3
95man/man3/BL_SAM_BUFF_INC_TOTAL_ALIGNMENTS.3 151man/man3/BL_SAM_BUFF_INC_TOTAL_ALIGNMENTS.3
96man/man3/BL_SAM_BUFF_INC_TRAILING_ALIGNMENTS.3 152man/man3/BL_SAM_BUFF_INC_TRAILING_ALIGNMENTS.3
97man/man3/BL_SAM_BUFF_MAPQ_HIGH.3 153man/man3/BL_SAM_BUFF_MAPQ_HIGH.3
98man/man3/BL_SAM_BUFF_MAPQ_LOW.3 154man/man3/BL_SAM_BUFF_MAPQ_LOW.3
99man/man3/BL_SAM_BUFF_MAPQ_MIN.3 155man/man3/BL_SAM_BUFF_MAPQ_MIN.3
100man/man3/BL_SAM_BUFF_MAPQ_SUM.3 156man/man3/BL_SAM_BUFF_MAPQ_SUM.3
 157man/man3/BL_SAM_BUFF_MAX_ALIGNMENTS.3
101man/man3/BL_SAM_BUFF_MAX_COUNT.3 158man/man3/BL_SAM_BUFF_MAX_COUNT.3
102man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3 159man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3
103man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3 160man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3
104man/man3/BL_SAM_BUFF_PREVIOUS_POS.3 161man/man3/BL_SAM_BUFF_PREVIOUS_POS.3
105man/man3/BL_SAM_BUFF_PREVIOUS_RNAME.3 162man/man3/BL_SAM_BUFF_PREVIOUS_RNAME.3
106man/man3/BL_SAM_BUFF_PREVIOUS_RNAME_AE.3 163man/man3/BL_SAM_BUFF_PREVIOUS_RNAME_AE.3
107man/man3/BL_SAM_BUFF_READS_USED.3 164man/man3/BL_SAM_BUFF_READS_USED.3
108man/man3/BL_SAM_BUFF_TOTAL_ALIGNMENTS.3 165man/man3/BL_SAM_BUFF_TOTAL_ALIGNMENTS.3
109man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3 166man/man3/BL_SAM_BUFF_TRAILING_ALIGNMENTS.3
110man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3 167man/man3/BL_SAM_BUFF_UNMAPPED_ALIGNMENTS.3
111man/man3/BL_SAM_CIGAR.3 168man/man3/BL_SAM_CIGAR.3
112man/man3/BL_SAM_CIGAR_AE.3 169man/man3/BL_SAM_CIGAR_AE.3
113man/man3/BL_SAM_FLAG.3 170man/man3/BL_SAM_FLAG.3
@@ -126,50 +183,55 @@ man/man3/BL_SAM_RNEXT_AE.3 @@ -126,50 +183,55 @@ man/man3/BL_SAM_RNEXT_AE.3
126man/man3/BL_SAM_SEQ.3 183man/man3/BL_SAM_SEQ.3
127man/man3/BL_SAM_SEQ_AE.3 184man/man3/BL_SAM_SEQ_AE.3
128man/man3/BL_SAM_SEQ_LEN.3 185man/man3/BL_SAM_SEQ_LEN.3
129man/man3/BL_SAM_TLEN.3 186man/man3/BL_SAM_TLEN.3
130man/man3/BL_VCF_ALT.3 187man/man3/BL_VCF_ALT.3
131man/man3/BL_VCF_ALT_AE.3 188man/man3/BL_VCF_ALT_AE.3
132man/man3/BL_VCF_ALT_COUNT.3 189man/man3/BL_VCF_ALT_COUNT.3
133man/man3/BL_VCF_CHROM.3 190man/man3/BL_VCF_CHROM.3
134man/man3/BL_VCF_CHROM_AE.3 191man/man3/BL_VCF_CHROM_AE.3
135man/man3/BL_VCF_FILTER.3 192man/man3/BL_VCF_FILTER.3
136man/man3/BL_VCF_FILTER_AE.3 193man/man3/BL_VCF_FILTER_AE.3
137man/man3/BL_VCF_FORMAT.3 194man/man3/BL_VCF_FORMAT.3
138man/man3/BL_VCF_FORMAT_AE.3 195man/man3/BL_VCF_FORMAT_AE.3
 196man/man3/BL_VCF_FORMAT_LEN.3
139man/man3/BL_VCF_FORMAT_MAX.3 197man/man3/BL_VCF_FORMAT_MAX.3
140man/man3/BL_VCF_ID.3 198man/man3/BL_VCF_ID.3
141man/man3/BL_VCF_ID_AE.3 199man/man3/BL_VCF_ID_AE.3
142man/man3/BL_VCF_INFO.3 200man/man3/BL_VCF_INFO.3
143man/man3/BL_VCF_INFO_AE.3 201man/man3/BL_VCF_INFO_AE.3
144man/man3/BL_VCF_INFO_LEN.3 202man/man3/BL_VCF_INFO_LEN.3
145man/man3/BL_VCF_INFO_MAX.3 203man/man3/BL_VCF_INFO_MAX.3
146man/man3/BL_VCF_MULTI_SAMPLES.3 204man/man3/BL_VCF_MULTI_SAMPLES.3
147man/man3/BL_VCF_MULTI_SAMPLES_AE.3 205man/man3/BL_VCF_MULTI_SAMPLES_AE.3
148man/man3/BL_VCF_OTHER_COUNT.3 206man/man3/BL_VCF_OTHER_COUNT.3
149man/man3/BL_VCF_PHREDS.3 207man/man3/BL_VCF_PHREDS.3
150man/man3/BL_VCF_PHREDS_AE.3 208man/man3/BL_VCF_PHREDS_AE.3
151man/man3/BL_VCF_PHRED_BUFF_SIZE.3 209man/man3/BL_VCF_PHRED_BUFF_SIZE.3
152man/man3/BL_VCF_PHRED_COUNT.3 210man/man3/BL_VCF_PHRED_COUNT.3
153man/man3/BL_VCF_POS.3 211man/man3/BL_VCF_POS.3
154man/man3/BL_VCF_QUAL.3 212man/man3/BL_VCF_QUAL.3
155man/man3/BL_VCF_QUAL_AE.3 213man/man3/BL_VCF_QUAL_AE.3
156man/man3/BL_VCF_REF.3 214man/man3/BL_VCF_REF.3
157man/man3/BL_VCF_REF_AE.3 215man/man3/BL_VCF_REF_AE.3
158man/man3/BL_VCF_REF_COUNT.3 216man/man3/BL_VCF_REF_COUNT.3
159man/man3/BL_VCF_SAMPLE_MAX.3 217man/man3/BL_VCF_SAMPLE_MAX.3
160man/man3/BL_VCF_SINGLE_SAMPLE.3 218man/man3/BL_VCF_SINGLE_SAMPLE.3
161man/man3/BL_VCF_SINGLE_SAMPLE_AE.3 219man/man3/BL_VCF_SINGLE_SAMPLE_AE.3
162man/man3/biolibc.3 220man/man3/biolibc.3
 221man/man3/bl_align_map_seq_exact.3
 222man/man3/bl_align_map_seq_sub.3
 223man/man3/bl_align_set_max_mismatch_percent.3
 224man/man3/bl_align_set_min_match.3
163man/man3/bl_bed_check_order.3 225man/man3/bl_bed_check_order.3
164man/man3/bl_bed_gff_cmp.3 226man/man3/bl_bed_gff_cmp.3
165man/man3/bl_bed_read.3 227man/man3/bl_bed_read.3
166man/man3/bl_bed_set_block_count.3 228man/man3/bl_bed_set_block_count.3
167man/man3/bl_bed_set_block_sizes.3 229man/man3/bl_bed_set_block_sizes.3
168man/man3/bl_bed_set_block_sizes_ae.3 230man/man3/bl_bed_set_block_sizes_ae.3
169man/man3/bl_bed_set_block_sizes_cpy.3 231man/man3/bl_bed_set_block_sizes_cpy.3
170man/man3/bl_bed_set_block_starts.3 232man/man3/bl_bed_set_block_starts.3
171man/man3/bl_bed_set_block_starts_ae.3 233man/man3/bl_bed_set_block_starts_ae.3
172man/man3/bl_bed_set_block_starts_cpy.3 234man/man3/bl_bed_set_block_starts_cpy.3
173man/man3/bl_bed_set_chrom_ae.3 235man/man3/bl_bed_set_chrom_ae.3
174man/man3/bl_bed_set_chrom_cpy.3 236man/man3/bl_bed_set_chrom_cpy.3
175man/man3/bl_bed_set_chrom_end.3 237man/man3/bl_bed_set_chrom_end.3
@@ -190,28 +252,31 @@ man/man3/bl_fasta_free.3 @@ -190,28 +252,31 @@ man/man3/bl_fasta_free.3
190man/man3/bl_fasta_init.3 252man/man3/bl_fasta_init.3
191man/man3/bl_fasta_read.3 253man/man3/bl_fasta_read.3
192man/man3/bl_fasta_set_desc.3 254man/man3/bl_fasta_set_desc.3
193man/man3/bl_fasta_set_desc_ae.3 255man/man3/bl_fasta_set_desc_ae.3
194man/man3/bl_fasta_set_desc_array_size.3 256man/man3/bl_fasta_set_desc_array_size.3
195man/man3/bl_fasta_set_desc_cpy.3 257man/man3/bl_fasta_set_desc_cpy.3
196man/man3/bl_fasta_set_desc_len.3 258man/man3/bl_fasta_set_desc_len.3
197man/man3/bl_fasta_set_seq.3 259man/man3/bl_fasta_set_seq.3
198man/man3/bl_fasta_set_seq_ae.3 260man/man3/bl_fasta_set_seq_ae.3
199man/man3/bl_fasta_set_seq_array_size.3 261man/man3/bl_fasta_set_seq_array_size.3
200man/man3/bl_fasta_set_seq_cpy.3 262man/man3/bl_fasta_set_seq_cpy.3
201man/man3/bl_fasta_set_seq_len.3 263man/man3/bl_fasta_set_seq_len.3
202man/man3/bl_fasta_write.3 264man/man3/bl_fasta_write.3
 265man/man3/bl_fastq_3p_trim.3
 266man/man3/bl_fastq_find_3p_low_qual.3
203man/man3/bl_fastq_free.3 267man/man3/bl_fastq_free.3
204man/man3/bl_fastq_init.3 268man/man3/bl_fastq_init.3
 269man/man3/bl_fastq_name_cmp.3
205man/man3/bl_fastq_read.3 270man/man3/bl_fastq_read.3
206man/man3/bl_fastq_set_desc.3 271man/man3/bl_fastq_set_desc.3
207man/man3/bl_fastq_set_desc_ae.3 272man/man3/bl_fastq_set_desc_ae.3
208man/man3/bl_fastq_set_desc_array_size.3 273man/man3/bl_fastq_set_desc_array_size.3
209man/man3/bl_fastq_set_desc_cpy.3 274man/man3/bl_fastq_set_desc_cpy.3
210man/man3/bl_fastq_set_desc_len.3 275man/man3/bl_fastq_set_desc_len.3
211man/man3/bl_fastq_set_plus.3 276man/man3/bl_fastq_set_plus.3
212man/man3/bl_fastq_set_plus_ae.3 277man/man3/bl_fastq_set_plus_ae.3
213man/man3/bl_fastq_set_plus_array_size.3 278man/man3/bl_fastq_set_plus_array_size.3
214man/man3/bl_fastq_set_plus_cpy.3 279man/man3/bl_fastq_set_plus_cpy.3
215man/man3/bl_fastq_set_plus_len.3 280man/man3/bl_fastq_set_plus_len.3
216man/man3/bl_fastq_set_qual.3 281man/man3/bl_fastq_set_qual.3
217man/man3/bl_fastq_set_qual_ae.3 282man/man3/bl_fastq_set_qual_ae.3
@@ -225,48 +290,73 @@ man/man3/bl_fastq_set_seq_cpy.3 @@ -225,48 +290,73 @@ man/man3/bl_fastq_set_seq_cpy.3
225man/man3/bl_fastq_set_seq_len.3 290man/man3/bl_fastq_set_seq_len.3
226man/man3/bl_fastq_write.3 291man/man3/bl_fastq_write.3
227man/man3/bl_fastx_desc.3 292man/man3/bl_fastx_desc.3
228man/man3/bl_fastx_desc_len.3 293man/man3/bl_fastx_desc_len.3
229man/man3/bl_fastx_free.3 294man/man3/bl_fastx_free.3
230man/man3/bl_fastx_init.3 295man/man3/bl_fastx_init.3
231man/man3/bl_fastx_plus.3 296man/man3/bl_fastx_plus.3
232man/man3/bl_fastx_plus_len.3 297man/man3/bl_fastx_plus_len.3
233man/man3/bl_fastx_qual.3 298man/man3/bl_fastx_qual.3
234man/man3/bl_fastx_qual_len.3 299man/man3/bl_fastx_qual_len.3
235man/man3/bl_fastx_read.3 300man/man3/bl_fastx_read.3
236man/man3/bl_fastx_seq.3 301man/man3/bl_fastx_seq.3
237man/man3/bl_fastx_seq_len.3 302man/man3/bl_fastx_seq_len.3
 303man/man3/bl_fastx_set_fasta.3
 304man/man3/bl_fastx_set_fastq.3
 305man/man3/bl_fastx_set_format.3
238man/man3/bl_fastx_write.3 306man/man3/bl_fastx_write.3
 307man/man3/bl_gff_copy_header.3
 308man/man3/bl_gff_extract_attribute.3
 309man/man3/bl_gff_free.3
 310man/man3/bl_gff_index_add.3
 311man/man3/bl_gff_index_seek_reverse.3
 312man/man3/bl_gff_index_set_array_size.3
 313man/man3/bl_gff_index_set_count.3
 314man/man3/bl_gff_index_set_end.3
 315man/man3/bl_gff_index_set_end_ae.3
 316man/man3/bl_gff_index_set_end_cpy.3
 317man/man3/bl_gff_index_set_file_pos.3
 318man/man3/bl_gff_index_set_file_pos_ae.3
 319man/man3/bl_gff_index_set_file_pos_cpy.3
 320man/man3/bl_gff_index_set_seqid.3
 321man/man3/bl_gff_index_set_seqid_ae.3
 322man/man3/bl_gff_index_set_seqid_cpy.3
 323man/man3/bl_gff_index_set_start.3
 324man/man3/bl_gff_index_set_start_ae.3
 325man/man3/bl_gff_index_set_start_cpy.3
 326man/man3/bl_gff_init.3
239man/man3/bl_gff_read.3 327man/man3/bl_gff_read.3
240man/man3/bl_gff_set_attributes.3 328man/man3/bl_gff_set_attributes.3
241man/man3/bl_gff_set_attributes_ae.3 329man/man3/bl_gff_set_attributes_ae.3
242man/man3/bl_gff_set_attributes_cpy.3 330man/man3/bl_gff_set_attributes_cpy.3
243man/man3/bl_gff_set_end.3 331man/man3/bl_gff_set_end.3
244man/man3/bl_gff_set_feature_ae.3 
245man/man3/bl_gff_set_feature_cpy.3 
246man/man3/bl_gff_set_feature_id.3 332man/man3/bl_gff_set_feature_id.3
247man/man3/bl_gff_set_feature_id_ae.3 333man/man3/bl_gff_set_feature_id_ae.3
248man/man3/bl_gff_set_feature_id_cpy.3 334man/man3/bl_gff_set_feature_id_cpy.3
249man/man3/bl_gff_set_gene_name.3 335man/man3/bl_gff_set_feature_name.3
250man/man3/bl_gff_set_gene_name_ae.3 336man/man3/bl_gff_set_feature_name_ae.3
 337man/man3/bl_gff_set_feature_name_cpy.3
 338man/man3/bl_gff_set_file_pos.3
251man/man3/bl_gff_set_gene_name_cpy.3 339man/man3/bl_gff_set_gene_name_cpy.3
252man/man3/bl_gff_set_phase.3 340man/man3/bl_gff_set_phase.3
253man/man3/bl_gff_set_score.3 341man/man3/bl_gff_set_score.3
254man/man3/bl_gff_set_sequence_ae.3 342man/man3/bl_gff_set_seqid_ae.3
255man/man3/bl_gff_set_sequence_cpy.3 343man/man3/bl_gff_set_seqid_cpy.3
256man/man3/bl_gff_set_source_ae.3 344man/man3/bl_gff_set_source_ae.3
257man/man3/bl_gff_set_source_cpy.3 345man/man3/bl_gff_set_source_cpy.3
258man/man3/bl_gff_set_start.3 346man/man3/bl_gff_set_start.3
259man/man3/bl_gff_set_strand.3 347man/man3/bl_gff_set_strand.3
 348man/man3/bl_gff_set_type_ae.3
 349man/man3/bl_gff_set_type_cpy.3
260man/man3/bl_gff_skip_header.3 350man/man3/bl_gff_skip_header.3
261man/man3/bl_gff_to_bed.3 351man/man3/bl_gff_to_bed.3
262man/man3/bl_gff_write.3 352man/man3/bl_gff_write.3
263man/man3/bl_next_start_codon.3 353man/man3/bl_next_start_codon.3
264man/man3/bl_next_stop_codon.3 354man/man3/bl_next_stop_codon.3
265man/man3/bl_overlap_print.3 355man/man3/bl_overlap_print.3
266man/man3/bl_overlap_set_all.3 356man/man3/bl_overlap_set_all.3
267man/man3/bl_overlap_set_feature1_len.3 357man/man3/bl_overlap_set_feature1_len.3
268man/man3/bl_overlap_set_feature2_len.3 358man/man3/bl_overlap_set_feature2_len.3
269man/man3/bl_overlap_set_overlap_end.3 359man/man3/bl_overlap_set_overlap_end.3
270man/man3/bl_overlap_set_overlap_len.3 360man/man3/bl_overlap_set_overlap_len.3
271man/man3/bl_overlap_set_overlap_start.3 361man/man3/bl_overlap_set_overlap_start.3
272man/man3/bl_pos_list_add_position.3 362man/man3/bl_pos_list_add_position.3
@@ -287,26 +377,27 @@ man/man3/bl_sam_buff_init.3 @@ -287,26 +377,27 @@ man/man3/bl_sam_buff_init.3
287man/man3/bl_sam_buff_out_of_order.3 377man/man3/bl_sam_buff_out_of_order.3
288man/man3/bl_sam_buff_set_alignments.3 378man/man3/bl_sam_buff_set_alignments.3
289man/man3/bl_sam_buff_set_alignments_ae.3 379man/man3/bl_sam_buff_set_alignments_ae.3
290man/man3/bl_sam_buff_set_alignments_cpy.3 380man/man3/bl_sam_buff_set_alignments_cpy.3
291man/man3/bl_sam_buff_set_buff_size.3 381man/man3/bl_sam_buff_set_buff_size.3
292man/man3/bl_sam_buff_set_buffered_count.3 382man/man3/bl_sam_buff_set_buffered_count.3
293man/man3/bl_sam_buff_set_discarded_alignments.3 383man/man3/bl_sam_buff_set_discarded_alignments.3
294man/man3/bl_sam_buff_set_discarded_score_sum.3 384man/man3/bl_sam_buff_set_discarded_score_sum.3
295man/man3/bl_sam_buff_set_discarded_trailing.3 385man/man3/bl_sam_buff_set_discarded_trailing.3
296man/man3/bl_sam_buff_set_mapq_high.3 386man/man3/bl_sam_buff_set_mapq_high.3
297man/man3/bl_sam_buff_set_mapq_low.3 387man/man3/bl_sam_buff_set_mapq_low.3
298man/man3/bl_sam_buff_set_mapq_min.3 388man/man3/bl_sam_buff_set_mapq_min.3
299man/man3/bl_sam_buff_set_mapq_sum.3 389man/man3/bl_sam_buff_set_mapq_sum.3
 390man/man3/bl_sam_buff_set_max_alignments.3
300man/man3/bl_sam_buff_set_max_count.3 391man/man3/bl_sam_buff_set_max_count.3
301man/man3/bl_sam_buff_set_max_discarded_score.3 392man/man3/bl_sam_buff_set_max_discarded_score.3
302man/man3/bl_sam_buff_set_min_discarded_score.3 393man/man3/bl_sam_buff_set_min_discarded_score.3
303man/man3/bl_sam_buff_set_previous_pos.3 394man/man3/bl_sam_buff_set_previous_pos.3
304man/man3/bl_sam_buff_set_previous_rname_ae.3 395man/man3/bl_sam_buff_set_previous_rname_ae.3
305man/man3/bl_sam_buff_set_previous_rname_cpy.3 396man/man3/bl_sam_buff_set_previous_rname_cpy.3
306man/man3/bl_sam_buff_set_reads_used.3 397man/man3/bl_sam_buff_set_reads_used.3
307man/man3/bl_sam_buff_set_total_alignments.3 398man/man3/bl_sam_buff_set_total_alignments.3
308man/man3/bl_sam_buff_set_trailing_alignments.3 399man/man3/bl_sam_buff_set_trailing_alignments.3
309man/man3/bl_sam_buff_set_unmapped_alignments.3 400man/man3/bl_sam_buff_set_unmapped_alignments.3
310man/man3/bl_sam_buff_shift.3 401man/man3/bl_sam_buff_shift.3
311man/man3/bl_sam_copy.3 402man/man3/bl_sam_copy.3
312man/man3/bl_sam_free.3 403man/man3/bl_sam_free.3
@@ -344,26 +435,27 @@ man/man3/bl_vcf_parse_field_spec.3 @@ -344,26 +435,27 @@ man/man3/bl_vcf_parse_field_spec.3
344man/man3/bl_vcf_read_ss_call.3 435man/man3/bl_vcf_read_ss_call.3
345man/man3/bl_vcf_read_static_fields.3 436man/man3/bl_vcf_read_static_fields.3
346man/man3/bl_vcf_sample_alloc.3 437man/man3/bl_vcf_sample_alloc.3
347man/man3/bl_vcf_set_alt_ae.3 438man/man3/bl_vcf_set_alt_ae.3
348man/man3/bl_vcf_set_alt_count.3 439man/man3/bl_vcf_set_alt_count.3
349man/man3/bl_vcf_set_alt_cpy.3 440man/man3/bl_vcf_set_alt_cpy.3
350man/man3/bl_vcf_set_chrom_ae.3 441man/man3/bl_vcf_set_chrom_ae.3
351man/man3/bl_vcf_set_chrom_cpy.3 442man/man3/bl_vcf_set_chrom_cpy.3
352man/man3/bl_vcf_set_filter_ae.3 443man/man3/bl_vcf_set_filter_ae.3
353man/man3/bl_vcf_set_filter_cpy.3 444man/man3/bl_vcf_set_filter_cpy.3
354man/man3/bl_vcf_set_format.3 445man/man3/bl_vcf_set_format.3
355man/man3/bl_vcf_set_format_ae.3 446man/man3/bl_vcf_set_format_ae.3
356man/man3/bl_vcf_set_format_cpy.3 447man/man3/bl_vcf_set_format_cpy.3
 448man/man3/bl_vcf_set_format_len.3
357man/man3/bl_vcf_set_format_max.3 449man/man3/bl_vcf_set_format_max.3
358man/man3/bl_vcf_set_id_ae.3 450man/man3/bl_vcf_set_id_ae.3
359man/man3/bl_vcf_set_id_cpy.3 451man/man3/bl_vcf_set_id_cpy.3
360man/man3/bl_vcf_set_info.3 452man/man3/bl_vcf_set_info.3
361man/man3/bl_vcf_set_info_ae.3 453man/man3/bl_vcf_set_info_ae.3
362man/man3/bl_vcf_set_info_cpy.3 454man/man3/bl_vcf_set_info_cpy.3
363man/man3/bl_vcf_set_info_len.3 455man/man3/bl_vcf_set_info_len.3
364man/man3/bl_vcf_set_info_max.3 456man/man3/bl_vcf_set_info_max.3
365man/man3/bl_vcf_set_multi_samples.3 457man/man3/bl_vcf_set_multi_samples.3
366man/man3/bl_vcf_set_multi_samples_ae.3 458man/man3/bl_vcf_set_multi_samples_ae.3
367man/man3/bl_vcf_set_multi_samples_cpy.3 459man/man3/bl_vcf_set_multi_samples_cpy.3
368man/man3/bl_vcf_set_other_count.3 460man/man3/bl_vcf_set_other_count.3
369man/man3/bl_vcf_set_phred_buff_size.3 461man/man3/bl_vcf_set_phred_buff_size.3
cvs diff -r1.7 -r1.8 pkgsrc/biology/biolibc/buildlink3.mk (expand / switch to unified diff)

--- pkgsrc/biology/biolibc/buildlink3.mk 2021/12/14 18:58:57 1.7
+++ pkgsrc/biology/biolibc/buildlink3.mk 2022/03/15 21:06:32 1.8
@@ -1,14 +1,14 @@ @@ -1,14 +1,14 @@
1# $NetBSD: buildlink3.mk,v 1.7 2021/12/14 18:58:57 bacon Exp $ 1# $NetBSD: buildlink3.mk,v 1.8 2022/03/15 21:06:32 bacon Exp $
2 2
3BUILDLINK_TREE+= biolibc 3BUILDLINK_TREE+= biolibc
4 4
5.if !defined(BIOLIBC_BUILDLINK3_MK) 5.if !defined(BIOLIBC_BUILDLINK3_MK)
6BIOLIBC_BUILDLINK3_MK:= 6BIOLIBC_BUILDLINK3_MK:=
7 7
8BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.2.1 8BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.2.2
9BUILDLINK_PKGSRCDIR.biolibc?= ../../biology/biolibc 9BUILDLINK_PKGSRCDIR.biolibc?= ../../biology/biolibc
10 10
11.include "../../devel/libxtend/buildlink3.mk" 11.include "../../devel/libxtend/buildlink3.mk"
12.endif # BIOLIBC_BUILDLINK3_MK 12.endif # BIOLIBC_BUILDLINK3_MK
13 13
14BUILDLINK_TREE+= -biolibc 14BUILDLINK_TREE+= -biolibc
cvs diff -r1.9 -r1.10 pkgsrc/biology/biolibc/distinfo (expand / switch to unified diff)

--- pkgsrc/biology/biolibc/distinfo 2021/12/14 18:58:57 1.9
+++ pkgsrc/biology/biolibc/distinfo 2022/03/15 21:06:32 1.10
@@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
1$NetBSD: distinfo,v 1.9 2021/12/14 18:58:57 bacon Exp $ 1$NetBSD: distinfo,v 1.10 2022/03/15 21:06:32 bacon Exp $
2 2
3BLAKE2s (biolibc-0.2.1.tar.gz) = e81198c3ae3185592c58cdd72b046db0bce898845bf4f850a46a35c2cadb09b6 3BLAKE2s (biolibc-0.2.2.tar.gz) = 41c301bb2c43693150b38629e5d8974589160334523783707f2daf3742dfc184
4SHA512 (biolibc-0.2.1.tar.gz) = 0743199591e6f3b8ea9986bbddcba972538925787aa01463236d9c7ec809860eb2ee5174bbc8f00d04e33d1802f7ff87f0d4fb010a21cb3a2eb6bb1978cb2647 4SHA512 (biolibc-0.2.2.tar.gz) = c9ae6e36e344686856a77d961aed628ee8f4f99be5c6740d017bbb3378437fce41a063ca2d6370a4173acce2e7d3f45fa4563d7e52dd8bc024b86458244129d2
5Size (biolibc-0.2.1.tar.gz) = 104282 bytes 5Size (biolibc-0.2.2.tar.gz) = 129251 bytes