From nobody Tue Mar 15 21:45:19 2022 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id D936E1A2D30F; Tue, 15 Mar 2022 21:45:19 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4KJ6QR5HH4z3QP5; Tue, 15 Mar 2022 21:45:19 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1647380719; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=V61PtSC8JLt5KYyvwnqEhoVwaHaNqhn02s9vcLE0dh4=; b=fSPEm50CI4HXVwTVvAvWQAxPgMjc7ZFETv2YFmlG8953ZCJf5giZQukJ6Cw8+LeF4er3c+ YbZlNX5zzJs4+oSzhGlni7ecufYFp4afQd+9aYci/7YqGdBJGc4ItrV4YFw3FrfnwCUuu2 /tHIpGnjp4KfhrGGDalsG052TdTzU1yha0PoYYjfe0NUfRqCcZtbTlulcmetrL9rnPv1sJ Bkd911cGPwxzN7c7xApBrJ3//0KlSoEuaeoYyc80Qa57tnERqyLrt90OnD8IPsLMxbAMOE fRZmSd/rXst0MygjIchxQrh27qvay5wqUcSQVCjXUKj7OX2FzkqaA1aRgDQZSA== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 931D01A9D; Tue, 15 Mar 2022 21:45:19 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 22FLjJnu058959; Tue, 15 Mar 2022 21:45:19 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 22FLjJIN058958; Tue, 15 Mar 2022 21:45:19 GMT (envelope-from git) Date: Tue, 15 Mar 2022 21:45:19 GMT Message-Id: <202203152145.22FLjJIN058958@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 258dc9d15d7c - main - biology/biolibc: Update to 0.2.2 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 258dc9d15d7c697fbe6fe4056a760360d36049a2 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1647380719; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=V61PtSC8JLt5KYyvwnqEhoVwaHaNqhn02s9vcLE0dh4=; b=VZLHl0rfS3MEwANfrYOPeFDkikskpLGfnteXfZ1umCHNW9q99FlXNOdT66e+73n6m+FLyf i59X/TkV7ApVRa7EZX8sQ/Pd7dR3K/YGTNY4bC7Uv1i2jTU4udMVlSP2Q/Ek9DB298m08W VKKF4kQf8bRPglLhfR68shQpRSHpsvGXf66x1UTCYHvIXzIHQPTsRJ8n/XWAHN3Z33dEDN eek+b/rzB6ilsOtl8PQ+DuWUnKfNx1pgXMqqslYJ2oc6s1Sq74mJrMYnhIggJrfzH+zSFb NSWXOWHRZW7vDT+pdUxO97ALCm4kCS7A3yk+wcTVa5MXlweSPdCWZd2uK9OyOQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1647380719; a=rsa-sha256; cv=none; b=L1MjL2uWYcQHB++pb/kMdC8wZD3eughgKdMlTpApXXJi2AZgOR7rRf90V2MfFwu6yDIaBE lHxkCdl4Y7XIX7//t4BmPiB+hfqgiF0Q88wp6ecsml1Hnvx99EAXsSZCsjlD1gwjXMe0Uw N9NQUCY5J6H7EII/433WrJJZeG4fc+iDtECjPJb4K7Ehik1cR9LF8N5hY11O+uZJa0JGXc mS/aqhL+yM6cMm2tMj2lbZk/25u7+Yg1SnJpyL/z/9w41WEUpRX57AuR45fVet8UCFoOhd U7n91UMU58i0Lha/zMiUXa/w9ABJ8xf4DNfIbqFkZNqPXRJu5j+wBXhq5fzXdQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=258dc9d15d7c697fbe6fe4056a760360d36049a2 commit 258dc9d15d7c697fbe6fe4056a760360d36049a2 Author: Jason W. Bacon AuthorDate: 2022-03-15 21:35:22 +0000 Commit: Jason W. Bacon CommitDate: 2022-03-15 21:35:22 +0000 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 --- biology/biolibc/Makefile | 2 +- biology/biolibc/distinfo | 6 +-- biology/biolibc/pkg-plist | 116 +++++++++++++++++++++++++++++++++++++++++----- 3 files changed, 108 insertions(+), 16 deletions(-) diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile index b9e0322a1721..465f7ea9a665 100644 --- a/biology/biolibc/Makefile +++ b/biology/biolibc/Makefile @@ -1,5 +1,5 @@ PORTNAME= biolibc -DISTVERSION= 0.2.1 +DISTVERSION= 0.2.2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo index a578ca9874ea..c319bf83d1ed 100644 --- a/biology/biolibc/distinfo +++ b/biology/biolibc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1639331819 -SHA256 (auerlab-biolibc-0.2.1_GH0.tar.gz) = c3a3ac20c549a7a7626c77bdb86e81bc01ece864c2818a1fa744614e81f9eda3 -SIZE (auerlab-biolibc-0.2.1_GH0.tar.gz) = 104282 +TIMESTAMP = 1647347323 +SHA256 (auerlab-biolibc-0.2.2_GH0.tar.gz) = b2d8ef23ce93321cc624fb1c7851e1353b12ac89ec0bac6a4f9ae0f3648869e4 +SIZE (auerlab-biolibc-0.2.2_GH0.tar.gz) = 129251 diff --git a/biology/biolibc/pkg-plist b/biology/biolibc/pkg-plist index e8cce147332e..c0167ab0df06 100644 --- a/biology/biolibc/pkg-plist +++ b/biology/biolibc/pkg-plist @@ -1,20 +1,60 @@ +include/biolibc/align-accessors.h +include/biolibc/align-mutators.h +include/biolibc/align-rvs.h +include/biolibc/align.h +include/biolibc/bed-accessors.h +include/biolibc/bed-mutators.h +include/biolibc/bed-rvs.h include/biolibc/bed.h include/biolibc/biolibc.h include/biolibc/biostring.h +include/biolibc/fasta-accessors.h +include/biolibc/fasta-mutators.h +include/biolibc/fasta-rvs.h include/biolibc/fasta.h +include/biolibc/fastq-accessors.h +include/biolibc/fastq-mutators.h +include/biolibc/fastq-rvs.h include/biolibc/fastq.h +include/biolibc/fastx-accessors.h +include/biolibc/fastx-mutators.h +include/biolibc/fastx-rvs.h include/biolibc/fastx.h +include/biolibc/gff-accessors.h +include/biolibc/gff-index-accessors.h +include/biolibc/gff-index-mutators.h +include/biolibc/gff-index-rvs.h +include/biolibc/gff-index.h +include/biolibc/gff-mutators.h +include/biolibc/gff-rvs.h include/biolibc/gff.h +include/biolibc/overlap-accessors.h +include/biolibc/overlap-mutators.h +include/biolibc/overlap-rvs.h include/biolibc/overlap.h +include/biolibc/pos-list-accessors.h +include/biolibc/pos-list-mutators.h +include/biolibc/pos-list-rvs.h include/biolibc/pos-list.h +include/biolibc/sam-accessors.h +include/biolibc/sam-buff-accessors.h +include/biolibc/sam-buff-mutators.h +include/biolibc/sam-buff-rvs.h include/biolibc/sam-buff.h +include/biolibc/sam-mutators.h +include/biolibc/sam-rvs.h include/biolibc/sam.h include/biolibc/translate.h +include/biolibc/vcf-accessors.h +include/biolibc/vcf-mutators.h +include/biolibc/vcf-rvs.h include/biolibc/vcf.h lib/libbiolibc.a lib/libbiolibc.so lib/libbiolibc.so.2 lib/libbiolibc.so.2.0 +man/man3/BL_ALIGN_MAX_MISMATCH_PERCENT.3.gz +man/man3/BL_ALIGN_MIN_MATCH.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 @@ -57,23 +97,39 @@ 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_FASTX_FASTA.3.gz +man/man3/BL_FASTX_FASTQ.3.gz +man/man3/BL_FASTX_FORMAT.3.gz +man/man3/BL_FASTX_UNION.3.gz +man/man3/BL_FASTX_}.3.gz man/man3/BL_GFF_ATTRIBUTES.3.gz man/man3/BL_GFF_ATTRIBUTES_AE.3.gz man/man3/BL_GFF_END.3.gz -man/man3/BL_GFF_FEATURE.3.gz -man/man3/BL_GFF_FEATURE_AE.3.gz man/man3/BL_GFF_FEATURE_ID.3.gz man/man3/BL_GFF_FEATURE_ID_AE.3.gz -man/man3/BL_GFF_GENE_NAME.3.gz -man/man3/BL_GFF_GENE_NAME_AE.3.gz +man/man3/BL_GFF_FEATURE_NAME.3.gz +man/man3/BL_GFF_FEATURE_NAME_AE.3.gz +man/man3/BL_GFF_FILE_POS.3.gz +man/man3/BL_GFF_INDEX_ARRAY_SIZE.3.gz +man/man3/BL_GFF_INDEX_COUNT.3.gz +man/man3/BL_GFF_INDEX_END.3.gz +man/man3/BL_GFF_INDEX_END_AE.3.gz +man/man3/BL_GFF_INDEX_FILE_POS.3.gz +man/man3/BL_GFF_INDEX_FILE_POS_AE.3.gz +man/man3/BL_GFF_INDEX_SEQID.3.gz +man/man3/BL_GFF_INDEX_SEQID_AE.3.gz +man/man3/BL_GFF_INDEX_START.3.gz +man/man3/BL_GFF_INDEX_START_AE.3.gz 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_SEQID.3.gz +man/man3/BL_GFF_SEQID_AE.3.gz man/man3/BL_GFF_SOURCE.3.gz man/man3/BL_GFF_SOURCE_AE.3.gz man/man3/BL_GFF_START.3.gz man/man3/BL_GFF_STRAND.3.gz +man/man3/BL_GFF_TYPE.3.gz +man/man3/BL_GFF_TYPE_AE.3.gz man/man3/BL_OVERLAP_FEATURE1_LEN.3.gz man/man3/BL_OVERLAP_FEATURE2_LEN.3.gz man/man3/BL_OVERLAP_OVERLAP_END.3.gz @@ -97,6 +153,7 @@ man/man3/BL_SAM_BUFF_MAPQ_HIGH.3.gz man/man3/BL_SAM_BUFF_MAPQ_LOW.3.gz man/man3/BL_SAM_BUFF_MAPQ_MIN.3.gz man/man3/BL_SAM_BUFF_MAPQ_SUM.3.gz +man/man3/BL_SAM_BUFF_MAX_ALIGNMENTS.3.gz man/man3/BL_SAM_BUFF_MAX_COUNT.3.gz man/man3/BL_SAM_BUFF_MAX_DISCARDED_SCORE.3.gz man/man3/BL_SAM_BUFF_MIN_DISCARDED_SCORE.3.gz @@ -135,6 +192,7 @@ man/man3/BL_VCF_FILTER.3.gz man/man3/BL_VCF_FILTER_AE.3.gz man/man3/BL_VCF_FORMAT.3.gz man/man3/BL_VCF_FORMAT_AE.3.gz +man/man3/BL_VCF_FORMAT_LEN.3.gz man/man3/BL_VCF_FORMAT_MAX.3.gz man/man3/BL_VCF_ID.3.gz man/man3/BL_VCF_ID_AE.3.gz @@ -159,6 +217,10 @@ man/man3/BL_VCF_SAMPLE_MAX.3.gz man/man3/BL_VCF_SINGLE_SAMPLE.3.gz man/man3/BL_VCF_SINGLE_SAMPLE_AE.3.gz man/man3/biolibc.3.gz +man/man3/bl_align_map_seq_exact.3.gz +man/man3/bl_align_map_seq_sub.3.gz +man/man3/bl_align_set_max_mismatch_percent.3.gz +man/man3/bl_align_set_min_match.3.gz man/man3/bl_bed_check_order.3.gz man/man3/bl_bed_gff_cmp.3.gz man/man3/bl_bed_read.3.gz @@ -199,8 +261,11 @@ 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_fasta_write.3.gz +man/man3/bl_fastq_3p_trim.3.gz +man/man3/bl_fastq_find_3p_low_qual.3.gz man/man3/bl_fastq_free.3.gz man/man3/bl_fastq_init.3.gz +man/man3/bl_fastq_name_cmp.3.gz man/man3/bl_fastq_read.3.gz man/man3/bl_fastq_set_desc.3.gz man/man3/bl_fastq_set_desc_ae.3.gz @@ -234,28 +299,53 @@ man/man3/bl_fastx_qual_len.3.gz man/man3/bl_fastx_read.3.gz man/man3/bl_fastx_seq.3.gz man/man3/bl_fastx_seq_len.3.gz +man/man3/bl_fastx_set_fasta.3.gz +man/man3/bl_fastx_set_fastq.3.gz +man/man3/bl_fastx_set_format.3.gz man/man3/bl_fastx_write.3.gz +man/man3/bl_gff_copy_header.3.gz +man/man3/bl_gff_extract_attribute.3.gz +man/man3/bl_gff_free.3.gz +man/man3/bl_gff_index_add.3.gz +man/man3/bl_gff_index_seek_reverse.3.gz +man/man3/bl_gff_index_set_array_size.3.gz +man/man3/bl_gff_index_set_count.3.gz +man/man3/bl_gff_index_set_end.3.gz +man/man3/bl_gff_index_set_end_ae.3.gz +man/man3/bl_gff_index_set_end_cpy.3.gz +man/man3/bl_gff_index_set_file_pos.3.gz +man/man3/bl_gff_index_set_file_pos_ae.3.gz +man/man3/bl_gff_index_set_file_pos_cpy.3.gz +man/man3/bl_gff_index_set_seqid.3.gz +man/man3/bl_gff_index_set_seqid_ae.3.gz +man/man3/bl_gff_index_set_seqid_cpy.3.gz +man/man3/bl_gff_index_set_start.3.gz +man/man3/bl_gff_index_set_start_ae.3.gz +man/man3/bl_gff_index_set_start_cpy.3.gz +man/man3/bl_gff_init.3.gz man/man3/bl_gff_read.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_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_feature_name.3.gz +man/man3/bl_gff_set_feature_name_ae.3.gz +man/man3/bl_gff_set_feature_name_cpy.3.gz +man/man3/bl_gff_set_file_pos.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_ae.3.gz -man/man3/bl_gff_set_sequence_cpy.3.gz +man/man3/bl_gff_set_seqid_ae.3.gz +man/man3/bl_gff_set_seqid_cpy.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_set_type_ae.3.gz +man/man3/bl_gff_set_type_cpy.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 @@ -296,6 +386,7 @@ 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_alignments.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 @@ -353,6 +444,7 @@ 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_len.3.gz man/man3/bl_vcf_set_format_max.3.gz man/man3/bl_vcf_set_id_ae.3.gz man/man3/bl_vcf_set_id_cpy.3.gz