git: 9876430959ae - main - biology/biolibc: Update to 0.2.0

Jason W. Bacon jwb at FreeBSD.org
Sat Aug 28 01:35:27 UTC 2021 

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=9876430959ae7d730e71ada0c6319e8deede88bc

commit 9876430959ae7d730e71ada0c6319e8deede88bc
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-08-28 01:21:02 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-08-28 01:21:02 +0000

    biology/biolibc: Update to 0.2.0
    
    Major API overhaul
    New classes for FASTA and FASTQ
    Generate accessor and mutator functions for all classes
    Generate man pages for all functions and macros
    Export delimiter-separated-value class to libxtend
---
 biology/biolibc/Makefile  |   2 +-
 biology/biolibc/distinfo  |   6 +-
 biology/biolibc/pkg-descr |   2 +-
 biology/biolibc/pkg-plist | 565 ++++++++++++++++++++++++++++++++++++++++++++--
 4 files changed, 553 insertions(+), 22 deletions(-)

diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile
index 821cfee94e6a..053f5dd838bc 100644
--- a/biology/biolibc/Makefile
+++ b/biology/biolibc/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	biolibc
-DISTVERSION=	0.1.3
+DISTVERSION=	0.2.0
 CATEGORIES=	biology
 
 MAINTAINER=	jwb at FreeBSD.org
diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo
index 2efe35731481..dbf9cb01d271 100644
--- a/biology/biolibc/distinfo
+++ b/biology/biolibc/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1623416887
-SHA256 (auerlab-biolibc-0.1.3_GH0.tar.gz) = 746a85a0e5ce9523fb0811cdbb36b4a4c8033190a2deb7e6b7b2566c12769ab7
-SIZE (auerlab-biolibc-0.1.3_GH0.tar.gz) = 30046
+TIMESTAMP = 1630025170
+SHA256 (auerlab-biolibc-0.2.0_GH0.tar.gz) = aa75db6b191ee1d461282235defd8b7c244a2b0f5cfecdecd4bbe14f1a20e73b
+SIZE (auerlab-biolibc-0.2.0_GH0.tar.gz) = 117553
diff --git a/biology/biolibc/pkg-descr b/biology/biolibc/pkg-descr
index 498258899832..25ace775ec47 100644
--- a/biology/biolibc/pkg-descr
+++ b/biology/biolibc/pkg-descr
@@ -4,4 +4,4 @@ general-purpose functions which could be used by a wide variety of
 applications.  These include functions for streaming common file formats such
 as SAM and VCF, string functions specific to bioinformatics, etc.
 
-WWW: https://github.com/auerlab/vcfio
+WWW: https://github.com/auerlab/biolibc
diff --git a/biology/biolibc/pkg-plist b/biology/biolibc/pkg-plist
index 5e508df38c26..c871ae3b95ff 100644
--- a/biology/biolibc/pkg-plist
+++ b/biology/biolibc/pkg-plist
@@ -1,8 +1,12 @@
 include/biolibc/bed.h
 include/biolibc/biolibc.h
-include/biolibc/dsv.h
+include/biolibc/biostring.h
+include/biolibc/fasta.h
+include/biolibc/fastq.h
+include/biolibc/fastx.h
 include/biolibc/gff.h
-include/biolibc/plist.h
+include/biolibc/overlap.h
+include/biolibc/pos-list.h
 include/biolibc/sam-buff.h
 include/biolibc/sam.h
 include/biolibc/vcf.h
@@ -10,19 +14,546 @@ lib/libbiolibc.a
 lib/libbiolibc.so
 lib/libbiolibc.so.2
 lib/libbiolibc.so.2.0
-man/man3/bed_check_order.3.gz
-man/man3/bed_gff_cmp.3.gz
-man/man3/bed_read_feature.3.gz
-man/man3/bed_set_chromosome.3.gz
-man/man3/bed_set_end_pos.3.gz
-man/man3/bed_set_fields.3.gz
-man/man3/bed_set_name.3.gz
-man/man3/bed_set_rgb_str.3.gz
-man/man3/bed_set_score.3.gz
-man/man3/bed_set_start_pos.3.gz
-man/man3/bed_set_strand.3.gz
-man/man3/bed_set_thick_end_pos.3.gz
-man/man3/bed_set_thick_start_pos.3.gz
-man/man3/bed_skip_header.3.gz
-man/man3/bed_write_feature.3.gz
+man/man3/BL_BED_BLOCK_COUNT.3.gz
+man/man3/BL_BED_BLOCK_SIZES.3.gz
+man/man3/BL_BED_BLOCK_SIZES_AE.3.gz
+man/man3/BL_BED_BLOCK_STARTS.3.gz
+man/man3/BL_BED_BLOCK_STARTS_AE.3.gz
+man/man3/BL_BED_CHROM.3.gz
+man/man3/BL_BED_CHROM_AE.3.gz
+man/man3/BL_BED_CHROM_END.3.gz
+man/man3/BL_BED_CHROM_START.3.gz
+man/man3/BL_BED_FIELDS.3.gz
+man/man3/BL_BED_ITEM_RGB.3.gz
+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
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