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Finish Release-0.16.0
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Daniel Mapleson committed Apr 29, 2016
2 parents de55ecf + e99e9ec commit 9a37525
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Showing 38 changed files with 2,504 additions and 552 deletions.
13 changes: 11 additions & 2 deletions Makefile.am
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Expand Up @@ -39,6 +39,7 @@ dist_bin_SCRIPTS = scripts/analyse_alignments.py \
scripts/predict.snakefile \
scripts/read_gen.snakefile \
scripts/snakey.py \
scripts/soapsplice2bed.py \
scripts/spanki2bed.py \
scripts/spanki_filter.py \
scripts/split_error_classes.py \
Expand All @@ -55,8 +56,16 @@ dist_bin_SCRIPTS = scripts/analyse_alignments.py \
configdir = $(datadir)/portcullis
dist_config_DATA = \
data/default_filter.json \
data/selftrain_initial_neg.json \
data/selftrain_initial_pos.json
data/selftrain_initial_neg.layer1.json \
data/selftrain_initial_neg.layer2.json \
data/selftrain_initial_neg.layer3.json \
data/selftrain_initial_neg.layer4.json \
data/selftrain_initial_neg.layer5.json \
data/selftrain_initial_neg.layer6.json \
data/selftrain_initial_neg.layer7.json \
data/selftrain_initial_pos.layer1.json \
data/selftrain_initial_pos.layer2.json \
data/selftrain_initial_pos.layer3.json

# SRC DIRS
make_dirs=deps/htslib-1.3 deps/ranger-0.3.8 lib src tests
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3 changes: 2 additions & 1 deletion configure.ac
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Expand Up @@ -4,7 +4,7 @@

# Autoconf setup
AC_PREREQ([2.68])
AC_INIT([portcullis],[0.15.0],[daniel.mapleson@tgac.ac.uk],[portcullis],[http://www.tgac.ac.uk])
AC_INIT([portcullis],[0.16.0],[daniel.mapleson@tgac.ac.uk],[portcullis],[http://www.tgac.ac.uk])
AC_CONFIG_SRCDIR([src/portcullis.cc])
AC_CONFIG_AUX_DIR([build-aux])
AC_CONFIG_MACRO_DIR([m4])
Expand Down Expand Up @@ -143,6 +143,7 @@ AX_BOOST_CHRONO
AX_BOOST_PROGRAM_OPTIONS
AX_BOOST_TIMER


# Combine BOOST variables
BOOST_LIBS="${BOOST_TIMER_STATIC_LIB} ${BOOST_CHRONO_STATIC_LIB} ${BOOST_FILESYSTEM_STATIC_LIB} ${BOOST_PROGRAM_OPTIONS_STATIC_LIB} ${BOOST_SYSTEM_STATIC_LIB}"
AC_SUBST([BOOST_LIBS])
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20 changes: 12 additions & 8 deletions data/selftrain_initial_neg.json → data/selftrain_initial_neg.json.old
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Expand Up @@ -9,20 +9,24 @@
"value": 1
},
"M3-nb_dist_aln": {
"operator": "eq",
"value": 1
"operator": "gte",
"value": 2
},
"M4-nb_rel_aln": {
"operator": "eq",
"value": 0
},
"M11-entropy": {
"operator": "eq",
"value": 0.0
"operator": "lt",
"value": 1.0
},
"M12-maxmmes": {
"operator": "lt",
"value": 8
"value": 9
},
"M12-maxmmes.2": {
"operator": "lte",
"value": 12
},
"M8-max_min_anc": {
"operator": "lt",
Expand All @@ -38,16 +42,16 @@
},
"M13-hamming5p": {
"operator": "lte",
"value": 1
"value": 2
},
"M14-hamming3p": {
"operator": "lte",
"value": 1
"value": 2
},
"M19-mean_mismatches": {
"operator": "gte",
"value": 5.0
}
},
"expression": "M2-nb_reads | M12-maxmmes | Suspect"
"expression": "M19-mean_mismatches | ( M1-canonical_ss & M11-entropy ) | ( M4-nb_rel_aln & M11-entropy ) | ( M12-maxmmes & M11-entropy ) | ( M12-maxmmes.2 & M2-nb_reads ) | ( M13-hamming5p & M14-hamming3p ) | PFP | ( Suspect & M2-nb_reads )"
}
93 changes: 93 additions & 0 deletions data/selftrain_initial_neg.layer1.json
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@@ -0,0 +1,93 @@
{
"parameters": {
"M1-canonical_ss": {
"operator": "in",
"value": ["N", "S"]
},
"M2-nb_reads": {
"operator": "lte",
"value": 1
},
"M3-nb_dist_aln": {
"operator": "gte",
"value": 2
},
"M4-nb_rel_aln": {
"operator": "eq",
"value": 0
},
"M11-entropy": {
"operator": "lt",
"value": 1.0
},
"M11-entropy.2": {
"operator": "gt",
"value": 2.0
},
"M11-entropy.3": {
"operator": "eq",
"value": 0.0
},
"M12-maxmmes": {
"operator": "lt",
"value": 7
},
"M12-maxmmes.2": {
"operator": "lt",
"value": 10
},
"M12-maxmmes.3": {
"operator": "lt",
"value": 20
},
"M8-max_min_anc": {
"operator": "lt",
"value": 16
},
"Suspect": {
"operator": "eq",
"value": 1
},
"PFP": {
"operator": "eq",
"value": 1
},
"M13-hamming5p": {
"operator": "lte",
"value": 2
},
"M14-hamming3p": {
"operator": "lte",
"value": 2
},
"M19-mean_mismatches": {
"operator": "gte",
"value": 5.0
},
"M19-mean_mismatches.2": {
"operator": "gte",
"value": 2.0
},
"M20-nb_usrs": {
"operator": "eq",
"value": 0
},
"M20-nb_usrs.2": {
"operator": "eq",
"value": 1
},
"M21-nb_msrs": {
"operator": "gte",
"value": 1
},
"M22-rel2raw": {
"operator": "lt",
"value": 0.9
},
"M22-rel2raw.2": {
"operator": "eq",
"value": 0.0
}
},
"expression": "( M20-nb_usrs & M21-nb_msrs & M12-maxmmes.2 & M22-rel2raw.2 )"
}
93 changes: 93 additions & 0 deletions data/selftrain_initial_neg.layer2.json
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@@ -0,0 +1,93 @@
{
"parameters": {
"M1-canonical_ss": {
"operator": "in",
"value": ["N", "S"]
},
"M2-nb_reads": {
"operator": "lte",
"value": 1
},
"M3-nb_dist_aln": {
"operator": "gte",
"value": 2
},
"M4-nb_rel_aln": {
"operator": "eq",
"value": 0
},
"M11-entropy": {
"operator": "lt",
"value": 1.0
},
"M11-entropy.2": {
"operator": "gt",
"value": 2.0
},
"M11-entropy.3": {
"operator": "eq",
"value": 0.0
},
"M12-maxmmes": {
"operator": "lt",
"value": 7
},
"M12-maxmmes.2": {
"operator": "lt",
"value": 10
},
"M12-maxmmes.3": {
"operator": "lt",
"value": 20
},
"M8-max_min_anc": {
"operator": "lt",
"value": 16
},
"Suspect": {
"operator": "eq",
"value": 1
},
"PFP": {
"operator": "eq",
"value": 1
},
"M13-hamming5p": {
"operator": "lte",
"value": 2
},
"M14-hamming3p": {
"operator": "lte",
"value": 2
},
"M19-mean_mismatches": {
"operator": "gte",
"value": 5.0
},
"M19-mean_mismatches.2": {
"operator": "gte",
"value": 2.0
},
"M20-nb_usrs": {
"operator": "eq",
"value": 0
},
"M20-nb_usrs.2": {
"operator": "eq",
"value": 1
},
"M21-nb_msrs": {
"operator": "gte",
"value": 1
},
"M22-rel2raw": {
"operator": "lt",
"value": 0.9
},
"M22-rel2raw.2": {
"operator": "eq",
"value": 0.0
}
},
"expression": "( M20-nb_usrs.2 & M1-canonical_ss & M12-maxmmes.2 )"
}
93 changes: 93 additions & 0 deletions data/selftrain_initial_neg.layer3.json
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@@ -0,0 +1,93 @@
{
"parameters": {
"M1-canonical_ss": {
"operator": "in",
"value": ["N", "S"]
},
"M2-nb_reads": {
"operator": "lte",
"value": 1
},
"M3-nb_dist_aln": {
"operator": "gte",
"value": 2
},
"M4-nb_rel_aln": {
"operator": "eq",
"value": 0
},
"M11-entropy": {
"operator": "lt",
"value": 1.0
},
"M11-entropy.2": {
"operator": "gt",
"value": 2.0
},
"M11-entropy.3": {
"operator": "eq",
"value": 0.0
},
"M12-maxmmes": {
"operator": "lt",
"value": 7
},
"M12-maxmmes.2": {
"operator": "lt",
"value": 10
},
"M12-maxmmes.3": {
"operator": "lt",
"value": 20
},
"M8-max_min_anc": {
"operator": "lt",
"value": 16
},
"Suspect": {
"operator": "eq",
"value": 1
},
"PFP": {
"operator": "eq",
"value": 1
},
"M13-hamming5p": {
"operator": "lte",
"value": 2
},
"M14-hamming3p": {
"operator": "lte",
"value": 2
},
"M19-mean_mismatches": {
"operator": "gte",
"value": 5.0
},
"M19-mean_mismatches.2": {
"operator": "gte",
"value": 2.0
},
"M20-nb_usrs": {
"operator": "eq",
"value": 0
},
"M20-nb_usrs.2": {
"operator": "eq",
"value": 1
},
"M21-nb_msrs": {
"operator": "gte",
"value": 1
},
"M22-rel2raw": {
"operator": "lt",
"value": 0.9
},
"M22-rel2raw.2": {
"operator": "eq",
"value": 0.0
}
},
"expression": "( Suspect & M11-entropy.2 )"
}
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