.hgignore
.hgtags
NEWS
README
ez_setup.py
setup.cfg
setup.py
doc/Makefile
doc/conf.py
doc/faq.rst
doc/gethelp.py
doc/index.rst
doc/make.bat
doc/quick.rst
doc/segway.rst
doc/support.rst
doc/technical.rst
doc/troubleshooting.rst
segway/__init__.py
segway/_configparser.py
segway/_util.py
segway/bed.py
segway/include.py
segway/input_master.py
segway/layer.py
segway/observations.py
segway/output.py
segway/run.py
segway/structure.py
segway/task.py
segway/winner.py
segway.egg-info/PKG-INFO
segway.egg-info/SOURCES.txt
segway.egg-info/dependency_links.txt
segway.egg-info/entry_points.txt
segway.egg-info/not-zip-safe
segway.egg-info/requires.txt
segway.egg-info/top_level.txt
segway/cluster/__init__.py
segway/cluster/common.py
segway/cluster/local.py
segway/cluster/lsf.py
segway/cluster/pbs.py
segway/cluster/sge.py
segway/cluster/sge_setup.py
segway/data/__init__.py
segway/data/dinucleotide.tmpl
segway/data/dont_train.list
segway/data/input.master.tmpl
segway/data/map_frameIndex_ruler.dt.txt
segway/data/map_segTransition_ruler_seg_segCountDown_segCountDown.dt.tmpl
segway/data/map_seg_segCountDown.dt.tmpl
segway/data/map_seg_subseg_obs.dt.txt
segway/data/map_supervisionLabel_seg_alwaysTrue_semisupervised.dt.txt
segway/data/observation.tmpl
segway/data/output.master
segway/data/seg_table.tab
segway/data/segway-clean.sh
segway/data/segway-wrapper.sh
segway/data/segway.inc.tmpl
segway/data/segway.str.tmpl
segway/data/supervision.tmpl
test/README
test/clean.sh
test/compare_directory.py
test/test_all.sh
test/00-pyflakes/flymake-pyflakes.sh
test/00-pyflakes/run.sh
test/data/run.sh
test/data/seg_table_min_100.tab
test/data/test.genomedata
test/data/touchstone/identifydir/posterior0.bedGraph.gz
test/data/touchstone/identifydir/posterior1.bedGraph.gz
test/data/touchstone/identifydir/posterior2.bedGraph.gz
test/data/touchstone/identifydir/posterior3.bedGraph.gz
test/data/touchstone/identifydir/segway.bed.gz
test/data/touchstone/identifydir/segway.layered.bed.gz
test/data/touchstone/identifydir/auxiliary/segway.inc
test/data/touchstone/identifydir/log/details.sh
test/data/touchstone/identifydir/log/jobs.tab
test/data/touchstone/identifydir/log/jt_info.posterior.txt
test/data/touchstone/identifydir/log/jt_info.txt
test/data/touchstone/identifydir/log/run.sh
test/data/touchstone/identifydir/log/segway.sh
test/data/touchstone/identifydir/observations/float32.list
test/data/touchstone/identifydir/observations/int.list
test/data/touchstone/identifydir/observations/observations.tab
test/data/touchstone/identifydir/output/e/identify/jt0.identifydir.(%[0-9a-f]{32}%)
test/data/touchstone/identifydir/output/e/identify/vit0.identifydir.(%[0-9a-f]{32}%)
test/data/touchstone/identifydir/output/o/identify/jt0.identifydir.(%[0-9a-f]{32}%)
test/data/touchstone/identifydir/output/o/identify/vit0.identifydir.(%[0-9a-f]{32}%)
test/data/touchstone/identifydir/posterior/posterior0.0.bed
test/data/touchstone/identifydir/posterior/posterior1.0.bed
test/data/touchstone/identifydir/posterior/posterior2.0.bed
test/data/touchstone/identifydir/posterior/posterior3.0.bed
test/data/touchstone/identifydir/posterior/posterior_code.0.bed
test/data/touchstone/identifydir/triangulation/segway.str.4.1.posterior.trifile
test/data/touchstone/identifydir/triangulation/segway.str.4.1.trifile
test/data/touchstone/identifydir/viterbi/viterbi0.bed
test/data/touchstone/traindir/segway.str
test/data/touchstone/traindir/train.tab
test/data/touchstone/traindir/accumulators/acc.0.0.bin
test/data/touchstone/traindir/auxiliary/dont_train.list
test/data/touchstone/traindir/auxiliary/segway.inc
test/data/touchstone/traindir/likelihood/likelihood.0.ll
test/data/touchstone/traindir/log/details.sh
test/data/touchstone/traindir/log/jobs.tab
test/data/touchstone/traindir/log/jt_info.txt
test/data/touchstone/traindir/log/likelihood.0.tab
test/data/touchstone/traindir/log/run.sh
test/data/touchstone/traindir/log/segway.sh
test/data/touchstone/traindir/observations/chr21.0000.float32
test/data/touchstone/traindir/observations/chr21.0000.int
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test/data/touchstone/traindir/params/input.master
test/data/touchstone/traindir/params/output.master
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test/data/touchstone/traindir/params/params.0.params.1
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test/data/touchstone/traindir/triangulation/segway.str.4.1.trifile
test/segway_layer/mnemonics
test/segway_layer/run.sh
test/segway_layer/segway.bed
test/segway_layer/touchstone/segway.layered.bed
test/segway_layer_bigbed/mnemonics
test/segway_layer_bigbed/run.sh
test/segway_layer_bigbed/segway.bed
test/segway_layer_bigbed/touchstone/segway.layered.bb
test/segway_layer_bigbed/touchstone/segway.layered.bed
test/segway_winner/chr1.fa
test/segway_winner/include-coords.bed
test/segway_winner/make-genomedata.sh
test/segway_winner/readme.txt
test/segway_winner/run.sh
test/segway_winner/segway_command.txt
test/segway_winner/simpleseg.genomedata
test/segway_winner/testtrack1.bedgraph
test/segway_winner/testtrack2.bedgraph
test/segway_winner/tracks.txt
test/segway_winner/traindir.tar.gz
test/segway_winner/touchstone/traindir/segway.str
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test/segway_winner/touchstone/traindir/log/segway.sh
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