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Viewing all changes in revision 1.

Committer: Bazaar Package Importer
Author(s): Shaun Jackman
Date: 2010-04-28 11:55:31 UTC
Revision ID: james.westby@ubuntu.com-20100428115531-xnhdigrc05e16xn4

Tags: upstream-2010-03-09

Import upstream version 2010-03-09

files added:

AUTHORS

COPYING

ChangeLog

INSTALL

Makefile.am

Makefile.in

NEWS

README

VERSION

acinclude.m4

aclocal.m4

config

config.site

config/acx_mmap_fixed.m4

config/acx_mmap_variable.m4

config/acx_pthread.m4

config/builtin.m4

config/compile

config/config.guess

config/config.sub

config/depcomp

config/expand.m4

config/fopen.m4

config/install-sh

config/ltmain.sh

config/madvise-flags.m4

config/missing

config/mkinstalldirs

config/mmap-flags.m4

config/pagesize.m4

config/perl.m4

config/struct-stat64.m4

configure

configure.ac

src

src/Makefile.am

src/Makefile.in

src/access.c

src/access.h

src/assert.c

src/assert.h

src/bigendian.c

src/bigendian.h

src/blackboard.c

src/blackboard.h

src/block.c

src/block.h

src/bool.h

src/boyer-moore.c

src/boyer-moore.h

src/changepoint.c

src/changepoint.h

src/chimera.c

src/chimera.h

src/chrnum.c

src/chrnum.h

src/chrom.c

src/chrom.h

src/chrsubset.c

src/chrsubset.h

src/cmet.c

src/cmet.h

src/cmetindex.c

src/comp.h

src/complement.h

src/compress.c

src/compress.h

src/config.h.in

src/datadir.c

src/datadir.h

src/diag.c

src/diag.h

src/diagdef.h

src/diagnostic.c

src/diagnostic.h

src/diagpool.c

src/diagpool.h

src/dibase.c

src/dibase.h

src/dibaseindex.c

src/dynprog.c

src/dynprog.h

src/except.c

src/except.h

src/fopen.h

src/gbuffer.c

src/gbuffer.h

src/genome-write.c

src/genome-write.h

src/genome.c

src/genome.h

src/genome_hr.c

src/genome_hr.h

src/genomicpos.c

src/genomicpos.h

src/get-genome.c

src/getopt.c

src/getopt.h

src/getopt1.c

src/gmap.c

src/gmapindex.c

src/gregion.c

src/gregion.h

src/gsnap.c

src/gsnap_tally.c

src/iit-read.c

src/iit-read.h

src/iit-write.c

src/iit-write.h

src/iit_dump.c

src/iit_get.c

src/iit_store.c

src/iitdef.h

src/indexdb.c

src/indexdb.h

src/indexdb_dibase.c

src/indexdb_dibase.h

src/indexdb_hr.c

src/indexdb_hr.h

src/indexdbdef.h

src/interval.c

src/interval.h

src/intlist.c

src/intlist.h

src/intlistdef.h

src/intpool.c

src/intpool.h

src/intron.c

src/intron.h

src/list.c

src/list.h

src/listdef.h

src/littleendian.c

src/littleendian.h

src/match.c

src/match.h

src/matchdef.h

src/matchpool.c

src/matchpool.h

src/maxent.c

src/maxent.h

src/md5.c

src/md5.h

src/mem.c

src/mem.h

src/oligo.c

src/oligo.h

src/oligoindex.c

src/oligoindex.h

src/orderstat.c

src/orderstat.h

src/pair.c

src/pair.h

src/pairdef.h

src/pairpool.c

src/pairpool.h

src/parserange.c

src/parserange.h

src/pbinom.c

src/pbinom.h

src/reader.c

src/reader.h

src/reqpost.c

src/reqpost.h

src/request.c

src/request.h

src/result.c

src/result.h

src/resulthr.c

src/resulthr.h

src/sam.c

src/sam.h

src/scores.h

src/segmentpos.c

src/segmentpos.h

src/separator.h

src/sequence.c

src/sequence.h

src/smooth.c

src/smooth.h

src/snpindex.c

src/spanningelt.c

src/spanningelt.h

src/stage1.c

src/stage1.h

src/stage1hr.c

src/stage1hr.h

src/stage2.c

src/stage2.h

src/stage3.c

src/stage3.h

src/stage3hr.c

src/stage3hr.h

src/stopwatch.c

src/stopwatch.h

src/substring.c

src/substring.h

src/table.c

src/table.h

src/tableint.c

src/tableint.h

src/translation.c

src/translation.h

src/types.h

src/uintlist.c

src/uintlist.h

tests

tests/Makefile.am

tests/Makefile.in

tests/align.test.in

tests/align.test.ok

tests/coords1.test.in

tests/coords1.test.ok

tests/defs

tests/fa.iittest

tests/iit.test.in

tests/iit_get.out.ok

tests/iittest.iit.ok

tests/map.test.ok

tests/setup.genomecomp.ok

tests/setup.ref3positions.ok

tests/setup1.test.in

tests/ss.chr17test

tests/ss.her2

util

util/Makefile.am

util/Makefile.in

util/fa_coords.pl.in

util/gmap_compress.pl.in

util/gmap_process.pl.in

util/gmap_reassemble.pl.in

util/gmap_setup.pl.in

util/gmap_uncompress.pl.in

util/gmap_update.pl.in

util/md_coords.pl.in

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added added

removed removed

config/acx_mmap_fixed.m4

config/acx_mmap_variable.m4

config/acx_pthread.m4

config/builtin.m4

config/config.guess

config/config.sub

config/expand.m4

config/fopen.m4

config/install-sh

config/ltmain.sh

config/madvise-flags.m4

config/mkinstalldirs

config/mmap-flags.m4

config/pagesize.m4

config/struct-stat64.m4

src/Makefile.am

src/Makefile.in

src/bigendian.c

src/bigendian.h

src/blackboard.c

src/blackboard.h

src/boyer-moore.c

src/boyer-moore.h

src/changepoint.c

src/changepoint.h

src/chrsubset.c

src/chrsubset.h

src/cmetindex.c

src/complement.h

src/config.h.in

src/diagnostic.c

src/diagnostic.h

src/dibaseindex.c

src/genome-write.c

src/genome-write.h

src/genome_hr.c

src/genome_hr.h

src/genomicpos.c

src/genomicpos.h

src/get-genome.c

src/gmapindex.c

src/gsnap_tally.c

src/iit-write.c

src/iit-write.h

src/iit_store.c

src/indexdb_dibase.c

src/indexdb_dibase.h

src/indexdb_hr.c

src/indexdb_hr.h

src/indexdbdef.h

src/intlistdef.h

src/littleendian.c

src/littleendian.h

src/matchpool.c

src/matchpool.h

src/oligoindex.c

src/oligoindex.h

src/orderstat.c

src/orderstat.h

src/parserange.c

src/parserange.h

src/segmentpos.c

src/segmentpos.h

src/separator.h

src/spanningelt.c

src/spanningelt.h

src/stopwatch.c

src/stopwatch.h

src/substring.c

src/substring.h

src/translation.c

src/translation.h

tests/Makefile.am

tests/Makefile.in

tests/align.test.in

tests/align.test.ok

tests/coords1.test.in

tests/coords1.test.ok

tests/fa.iittest

tests/iit.test.in

tests/iit_get.out.ok

tests/iittest.iit.ok

tests/map.test.ok

tests/setup.genomecomp.ok

tests/setup.ref3positions.ok

tests/setup1.test.in

tests/ss.chr17test

util/Makefile.am

util/Makefile.in

util/fa_coords.pl.in

util/gmap_compress.pl.in

util/gmap_process.pl.in

util/gmap_reassemble.pl.in

util/gmap_setup.pl.in

util/gmap_uncompress.pl.in

util/gmap_update.pl.in

util/md_coords.pl.in

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