[med-svn] [tigr-glimmer-mg] 05/06: Update upstream source from tag 'upstream/0.3.2'
Andreas Tille
tille at debian.org
Sun Dec 24 20:26:18 UTC 2017
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tille pushed a commit to branch master
in repository tigr-glimmer-mg.
commit 3c019c2b3bdad693f0bc451fde72dbb869f36267
Merge: 2535525 f12d344
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 24 21:11:49 2017 +0100
Update upstream source from tag 'upstream/0.3.2'
Update to upstream version '0.3.2'
with Debian dir c2bda7333e664573ea167ac91ebab3b3c0a8a7e6
LICENSE | 106 +
README | 37 +
data/phymm_dists.dat | 2243 +
docs/delcher.sty | 305 +
docs/notes.bib | 63 +
docs/notes.pdf | Bin 0 -> 198966 bytes
docs/notes.tex | 912 +
install_glimmer.py | 179 +
sample-run/glimmer-mg/map.txt | 999 +
sample-run/glimmer-mg/results/cluster-0.fa | 212 +
sample-run/glimmer-mg/results/cluster-0.icm | Bin 0 -> 440552 bytes
sample-run/glimmer-mg/results/cluster-1.fa | 1162 +
sample-run/glimmer-mg/results/cluster-1.icm | Bin 0 -> 480416 bytes
sample-run/glimmer-mg/results/cluster-2.fa | 184 +
sample-run/glimmer-mg/results/cluster-2.icm | Bin 0 -> 460704 bytes
sample-run/glimmer-mg/results/cluster-3.fa | 338 +
sample-run/glimmer-mg/results/cluster-3.icm | Bin 0 -> 470472 bytes
sample-run/glimmer-mg/results/cluster-4.fa | 28 +
sample-run/glimmer-mg/results/cluster-4.icm | Bin 0 -> 238768 bytes
sample-run/glimmer-mg/results/cluster-5.fa | 74 +
sample-run/glimmer-mg/results/cluster-5.icm | Bin 0 -> 412392 bytes
sample-run/glimmer-mg/results/icm-0.scores.tmp | 999 +
sample-run/glimmer-mg/results/icm-1.scores.tmp | 999 +
sample-run/glimmer-mg/results/icm-2.scores.tmp | 999 +
sample-run/glimmer-mg/results/icm-3.scores.tmp | 999 +
sample-run/glimmer-mg/results/icm-4.scores.tmp | 999 +
sample-run/glimmer-mg/results/icm-5.scores.tmp | 999 +
sample-run/glimmer-mg/results/immc.log | 3 +
.../glimmer-mg/results/rawPhymmOutput_seqs_fa.txt | 5489 ++
.../results/results.01.phymm_seqs_fa.txt | 1000 +
sample-run/glimmer-mg/results/sample.fa | 1 +
sample-run/glimmer-mg/results/seqs.class.txt | 999 +
.../glimmer-mg/results/seqs.cluster-0.class.txt | 106 +
.../glimmer-mg/results/seqs.cluster-0.predict | 240 +
.../results/seqs.cluster-0.run1.filt.features.txt | 10 +
.../results/seqs.cluster-0.run1.filt.gene.fasta | 260 +
.../results/seqs.cluster-0.run1.filt.gicm | Bin 0 -> 572244 bytes
.../results/seqs.cluster-0.run1.filt.motif | 5 +
.../results/seqs.cluster-0.run1.filt.predict | 236 +
.../glimmer-mg/results/seqs.cluster-0.run1.predict | 236 +
.../glimmer-mg/results/seqs.cluster-1.class.txt | 581 +
.../glimmer-mg/results/seqs.cluster-1.predict | 1299 +
.../results/seqs.cluster-1.run1.filt.features.txt | 10 +
.../results/seqs.cluster-1.run1.filt.gene.fasta | 1408 +
.../results/seqs.cluster-1.run1.filt.gicm | Bin 0 -> 1339692 bytes
.../results/seqs.cluster-1.run1.filt.motif | 5 +
.../results/seqs.cluster-1.run1.filt.predict | 1285 +
.../glimmer-mg/results/seqs.cluster-1.run1.predict | 1290 +
.../glimmer-mg/results/seqs.cluster-2.class.txt | 92 +
.../glimmer-mg/results/seqs.cluster-2.predict | 213 +
.../results/seqs.cluster-2.run1.filt.features.txt | 10 +
.../results/seqs.cluster-2.run1.filt.gene.fasta | 240 +
.../results/seqs.cluster-2.run1.filt.gicm | Bin 0 -> 667108 bytes
.../results/seqs.cluster-2.run1.filt.motif | 5 +
.../results/seqs.cluster-2.run1.filt.predict | 212 +
.../glimmer-mg/results/seqs.cluster-2.run1.predict | 213 +
.../glimmer-mg/results/seqs.cluster-3.class.txt | 169 +
.../glimmer-mg/results/seqs.cluster-3.predict | 373 +
.../results/seqs.cluster-3.run1.filt.features.txt | 10 +
.../results/seqs.cluster-3.run1.filt.gene.fasta | 406 +
.../results/seqs.cluster-3.run1.filt.gicm | Bin 0 -> 874348 bytes
.../results/seqs.cluster-3.run1.filt.motif | 5 +
.../results/seqs.cluster-3.run1.filt.predict | 372 +
.../glimmer-mg/results/seqs.cluster-3.run1.predict | 375 +
.../glimmer-mg/results/seqs.cluster-4.class.txt | 14 +
.../glimmer-mg/results/seqs.cluster-4.predict | 31 +
.../results/seqs.cluster-4.run1.filt.features.txt | 10 +
.../results/seqs.cluster-4.run1.filt.gene.fasta | 34 +
.../results/seqs.cluster-4.run1.filt.gicm | Bin 0 -> 153364 bytes
.../results/seqs.cluster-4.run1.filt.motif | 5 +
.../results/seqs.cluster-4.run1.filt.predict | 31 +
.../glimmer-mg/results/seqs.cluster-4.run1.predict | 32 +
.../glimmer-mg/results/seqs.cluster-5.class.txt | 37 +
.../glimmer-mg/results/seqs.cluster-5.predict | 76 +
.../results/seqs.cluster-5.run1.filt.features.txt | 10 +
.../results/seqs.cluster-5.run1.filt.gene.fasta | 74 +
.../results/seqs.cluster-5.run1.filt.gicm | Bin 0 -> 309740 bytes
.../results/seqs.cluster-5.run1.filt.motif | 5 +
.../results/seqs.cluster-5.run1.filt.predict | 74 +
.../glimmer-mg/results/seqs.cluster-5.run1.predict | 76 +
sample-run/glimmer-mg/results/seqs.predict | 2222 +
sample-run/glimmer-mg/results/seqs.run1.predict | 2222 +
sample-run/glimmer-mg/seqs.fa | 1998 +
sample-run/glimmer3/NC_000915.fna | 23828 ++++++
sample-run/glimmer3/NC_000915.gbk | 83961 +++++++++++++++++++
sample-run/glimmer3/results/NC_000915.icm | Bin 0 -> 1380524 bytes
sample-run/glimmer3/results/NC_000915.longorfs | 1161 +
.../glimmer3/results/NC_000915.run1.features.txt | 30023 +++++++
.../glimmer3/results/NC_000915.run1.gene.fasta | 3098 +
sample-run/glimmer3/results/NC_000915.run1.gicm | Bin 0 -> 1388532 bytes
sample-run/glimmer3/results/NC_000915.run1.motif | 5 +
sample-run/glimmer3/results/NC_000915.run1.predict | 1550 +
.../glimmer3/results/NC_000915.run2.features.txt | 19781 +++++
.../glimmer3/results/NC_000915.run2.gene.fasta | 3434 +
sample-run/glimmer3/results/NC_000915.run2.gicm | Bin 0 -> 1387740 bytes
sample-run/glimmer3/results/NC_000915.run2.motif | 5 +
sample-run/glimmer3/results/NC_000915.run2.predict | 1803 +
sample-run/glimmer3/results/NC_000915.train | 22507 +++++
scimm-0.3.0.tar.gz | Bin 0 -> 10438205 bytes
scripts/double_icms.py | 158 +
scripts/extract_aa.py | 391 +
scripts/g3-iterated.py | 100 +
scripts/get-motif-counts.awk | 28 +
scripts/glim-diff.awk | 137 +
scripts/glimmer-mg.py | 700 +
scripts/informative_genomes.py | 55 +
scripts/match-list-col.awk | 38 +
scripts/not-acgt.awk | 55 +
scripts/phymm_par.py | 507 +
scripts/scoreReadsGlim.pl | 1115 +
scripts/train_all.py | 96 +
scripts/train_features.py | 824 +
scripts/upstream-coords.awk | 65 +
src/Common/Makefile | 19 +
src/Common/delcher.cc | 412 +
src/Common/delcher.hh | 202 +
src/Common/exceptions.hh | 121 +
src/Common/fasta.cc | 286 +
src/Common/fasta.hh | 42 +
src/Common/gene.cc | 1627 +
src/Common/gene.hh | 359 +
src/Common/kelley.cc | 243 +
src/Common/kelley.hh | 22 +
src/Common/xlate_tables.hh | 156 +
src/Glimmer/Makefile | 26 +
src/Glimmer/anomaly.cc | 428 +
src/Glimmer/anomaly.hh | 32 +
src/Glimmer/glimmer-mg.cc | 2359 +
src/Glimmer/glimmer-mg.hh | 118 +
src/Glimmer/glimmer2.cc | 3756 +
src/Glimmer/glimmer3.cc | 1864 +
src/Glimmer/glimmer3.hh | 65 +
src/Glimmer/glimmer_base.cc | 2930 +
src/Glimmer/glimmer_base.hh | 311 +
src/Glimmer/long-orfs.cc | 1600 +
src/Glimmer/long-orfs.hh | 122 +
src/Glimmer/test.cc | 30 +
src/ICM/Makefile | 25 +
src/ICM/build-fixed.cc | 337 +
src/ICM/build-fixed.hh | 27 +
src/ICM/build-icm.cc | 406 +
src/ICM/build-icm.hh | 55 +
src/ICM/icm.cc | 2030 +
src/ICM/icm.hh | 307 +
src/ICM/score-fixed.cc | 241 +
src/ICM/score-fixed.hh | 24 +
src/Makefile | 29 +
src/Util/Makefile | 35 +
src/Util/entropy-fasta.cc | 141 +
src/Util/entropy-fasta.hh | 23 +
src/Util/entropy-profile.cc | 221 +
src/Util/entropy-profile.hh | 25 +
src/Util/entropy-score.cc | 400 +
src/Util/entropy-score.hh | 31 +
src/Util/extract.cc | 347 +
src/Util/extract.hh | 28 +
src/Util/multi-extract.cc | 408 +
src/Util/multi-extract.hh | 46 +
src/Util/start-codon-distrib.cc | 346 +
src/Util/start-codon-distrib.hh | 41 +
src/Util/uncovered.cc | 423 +
src/Util/uncovered.hh | 44 +
src/Util/window-acgt.cc | 288 +
src/Util/window-acgt.hh | 31 +
src/c_make.gen | 428 +
src/c_make.glm | 24 +
166 files changed, 256311 insertions(+)
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