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(-)biology/iolib/Makefile (-4 / +2 lines)
Lines 2-12 Link Here
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# $FreeBSD: head/biology/iolib/Makefile 351071 2014-04-12 07:42:33Z culot $
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# $FreeBSD: head/biology/iolib/Makefile 351071 2014-04-12 07:42:33Z culot $
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PORTNAME=	io_lib
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PORTNAME=	io_lib
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PORTVERSION=	1.13.0
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PORTVERSION=	1.13.5
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PORTREVISION=	1
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CATEGORIES=	biology
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CATEGORIES=	biology
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MASTER_SITES=	SF
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MASTER_SITES=	SF/staden/${PORTNAME}/${PORTVERSION}
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MASTER_SITE_SUBDIR=	staden/${PORTNAME}/${PORTVERSION}
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MAINTAINER=	ports@FreeBSD.org
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MAINTAINER=	ports@FreeBSD.org
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COMMENT=	General purpose trace file (and Experiment File) reading interface
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COMMENT=	General purpose trace file (and Experiment File) reading interface
(-)biology/iolib/distinfo (-2 / +2 lines)
Lines 1-2 Link Here
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SHA256 (io_lib-1.13.0.tar.gz) = c3e0106802bd1a4a41427304944bcf11b7a4dd249cf470454a35d30cde13db5c
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SHA256 (io_lib-1.13.5.tar.gz) = 3e30f1e972d3d75c4efa54032ceca975cea9733ce1eef3982ee8a2b9f799ba56
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SIZE (io_lib-1.13.0.tar.gz) = 1522227
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SIZE (io_lib-1.13.5.tar.gz) = 1808537
(-)biology/iolib/files/patch-progs__scram_flgstat.c (+10 lines)
Line 0 Link Here
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--- progs/scram_flagstat.c.orig
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+++ progs/scram_flagstat.c
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@@ -44,6 +44,7 @@
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 #include <assert.h>
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 #include <ctype.h>
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 #include <errno.h>
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+#include <unistd.h>
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 #if defined(__MINGW32__)
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 #   include <getopt.h>
(-)biology/iolib/pkg-plist (-37 / +38 lines)
Lines 1-8 Link Here
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bin/append_sff
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bin/convert_trace
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bin/cram_dump
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bin/cram_index
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bin/extract_fastq
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bin/extract_qual
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bin/extract_seq
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bin/get_comment
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bin/hash_exp
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bin/hash_extract
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bin/hash_list
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bin/hash_sff
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bin/hash_tar
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bin/index_tar
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bin/io_lib-config
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bin/makeSCF
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bin/scf_dump
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bin/scf_info
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bin/scf_update
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bin/scram_flagstat
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bin/scram_merge
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bin/scram_pileup
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bin/scramble
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bin/srf2fasta
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bin/srf2fastq
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bin/srf_dump_all
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bin/srf_extract_hash
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bin/srf_extract_linear
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bin/srf_filter
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bin/srf_index_hash
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bin/srf_info
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bin/srf_list
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bin/trace_dump
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bin/ztr_dump
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include/io_lib/Read.h
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include/io_lib/Read.h
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include/io_lib/abi.h
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include/io_lib/abi.h
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include/io_lib/alf.h
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include/io_lib/alf.h
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include/io_lib/array.h
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include/io_lib/array.h
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include/io_lib/bam.h
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include/io_lib/bam.h
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include/io_lib/binning.h
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include/io_lib/compress.h
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include/io_lib/compress.h
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include/io_lib/compression.h
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include/io_lib/compression.h
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include/io_lib/cram.h
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include/io_lib/cram.h
Lines 11-16 Link Here
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include/io_lib/cram_encode.h
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include/io_lib/cram_encode.h
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include/io_lib/cram_index.h
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include/io_lib/cram_index.h
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include/io_lib/cram_io.h
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include/io_lib/cram_io.h
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include/io_lib/cram_stats.h
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include/io_lib/cram_structs.h
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include/io_lib/cram_structs.h
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include/io_lib/deflate_interlaced.h
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include/io_lib/deflate_interlaced.h
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include/io_lib/dstring.h
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include/io_lib/dstring.h
Lines 33-89 Link Here
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include/io_lib/scf_extras.h
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include/io_lib/scf_extras.h
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include/io_lib/scram.h
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include/io_lib/scram.h
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include/io_lib/seqIOABI.h
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include/io_lib/seqIOABI.h
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include/io_lib/seqIOCTF.h
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include/io_lib/sff.h
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include/io_lib/sff.h
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include/io_lib/srf.h
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include/io_lib/srf.h
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include/io_lib/stdio_hack.h
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include/io_lib/stdio_hack.h
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include/io_lib/string_alloc.h
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include/io_lib/string_alloc.h
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include/io_lib/tar_format.h
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include/io_lib/tar_format.h
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include/io_lib/thread_pool.h
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include/io_lib/traceType.h
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include/io_lib/traceType.h
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include/io_lib/translate.h
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include/io_lib/translate.h
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include/io_lib/vlen.h
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include/io_lib/vlen.h
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include/io_lib/xalloc.h
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include/io_lib/xalloc.h
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include/io_lib/zfio.h
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include/io_lib/zfio.h
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include/io_lib/ztr.h
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include/io_lib/ztr.h
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bin/append_sff
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bin/convert_trace
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bin/cram_dump
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bin/cram_index
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bin/cram_to_sam
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bin/extract_fastq
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bin/extract_qual
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bin/extract_seq
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bin/get_comment
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bin/hash_exp
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bin/hash_extract
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bin/hash_list
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bin/hash_sff
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bin/hash_tar
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bin/index_tar
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bin/io_lib-config
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bin/makeSCF
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bin/sam_convert
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bin/sam_to_cram
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bin/scf_dump
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bin/scf_info
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bin/scf_update
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bin/scram_merge
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bin/scramble
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bin/srf2fasta
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bin/srf2fastq
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bin/srf_dump_all
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bin/srf_extract_hash
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bin/srf_extract_linear
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bin/srf_filter
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bin/srf_index_hash
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bin/srf_info
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bin/srf_list
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bin/trace_dump
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bin/ztr_dump
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lib/libstaden-read.a
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lib/libstaden-read.a
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lib/libstaden-read.la
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lib/libstaden-read.la
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lib/libstaden-read.so
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lib/libstaden-read.so
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lib/libstaden-read.so.3
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lib/libstaden-read.so.5
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man/man1/scramble.1.gz
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man/man1/scramble.1.gz
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man/man1/srf2fasta.1.gz
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man/man1/srf2fasta.1.gz
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man/man1/srf2fastq.1.gz
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man/man1/srf2fastq.1.gz

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