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Additional improvements to the filtering tool.
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Daniel Mapleson committed Apr 29, 2016
1 parent 999eafa commit 9404738
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Showing 7 changed files with 172 additions and 114 deletions.
4 changes: 3 additions & 1 deletion Makefile.am
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Expand Up @@ -62,8 +62,10 @@ dist_config_DATA = \
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.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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21 changes: 21 additions & 0 deletions data/selftrain_initial_neg.layer7.json
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@@ -0,0 +1,21 @@
{
"parameters": {
"M2-nb_reads": {
"operator": "gt",
"value": 100
},
"M22-rel2raw": {
"operator": "eq",
"value": 0.0
},
"M13-hamming5p": {
"operator": "lte",
"value": 4
},
"M14-hamming3p": {
"operator": "lte",
"value": 4
}
},
"expression": "( M2-nb_reads & M22-rel2raw & M13-hamming5p & M14-hamming3p )"
}
52 changes: 8 additions & 44 deletions data/selftrain_initial_pos.layer1.json
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@@ -1,69 +1,33 @@
{
"parameters": {
"M1-canonical_ss": {
"operator": "in",
"value": ["C", "S"]
},
"M1-canonical_ss.2": {
"operator": "in",
"value": ["N"]
},
"M4-nb_rel_aln": {
"operator": "gte",
"value": 5
},
"M4-nb_rel_aln.2": {
"operator": "gte",
"value": 1
},
"M12-maxmmes": {
"operator": "gte",
"value": 20
},
"M12-maxmmes.2": {
"operator": "gte",
"value": 10
"value": 8
},
"M11-entropy": {
"operator": "gt",
"value": 5.0
},
"M11-entropy.2": {
"operator": "gt",
"value": 2.0
},
"M13-hamming5p": {
"M13-hamming5p": {
"operator": "gte",
"value": 5
},
"M13-hamming5p.2": {
"operator": "gte",
"value": 7
},
"M14-hamming3p": {
"operator": "gte",
"value": 5
},
"M14-hamming3p.2": {
"operator": "gte",
"value": 7
},
"M19-mean_mismatches": {
"operator": "eq",
"value": 0
},
"M19-mean_mismatches.2": {
"operator": "lt",
"value": 0.2
"M19-mean_mismatches": {
"operator": "lte",
"value": 1.5
},
"M20-nb_usrs": {
"operator": "gte",
"value": 5
"value": 1
},
"M22-rel2raw": {
"operator": "gte",
"value": 0.5
"value": 0.25
}
},
"expression": "M4-nb_rel_aln & M13-hamming5p & M14-hamming3p & M22-rel2raw & M12-maxmmes.2"
"expression": "M4-nb_rel_aln & M13-hamming5p & M14-hamming3p & M12-maxmmes & M20-nb_usrs & M19-mean_mismatches & M22-rel2raw"
}
52 changes: 14 additions & 38 deletions data/selftrain_initial_pos.layer2.json
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@@ -1,69 +1,45 @@
{
"parameters": {
"M1-canonical_ss": {
"operator": "in",
"value": ["C", "S"]
},
"M1-canonical_ss.2": {
"operator": "in",
"value": ["N"]
},
"M4-nb_rel_aln": {
"operator": "gte",
"value": 5
"value": 3
},
"M4-nb_rel_aln.2": {
"operator": "gte",
"value": 1
"value": 2
},
"M12-maxmmes": {
"operator": "gte",
"value": 20
"value": 25
},
"M12-maxmmes.2": {
"operator": "gte",
"value": 10
"operator": "gt",
"value": 12
},
"M11-entropy": {
"operator": "gt",
"value": 5.0
},
"M11-entropy.2": {
"operator": "gt",
"value": 2.0
},
"M13-hamming5p": {
"operator": "gte",
"value": 5
"value": 8
},
"M13-hamming5p.2": {
"operator": "gte",
"value": 7
"value": 10
},
"M14-hamming3p": {
"operator": "gte",
"value": 5
"value": 8
},
"M14-hamming3p.2": {
"operator": "gte",
"value": 7
"value": 10
},
"M19-mean_mismatches": {
"operator": "eq",
"M19-mean_mismatches": {
"operator": "lt",
"value": 0
},
"M19-mean_mismatches.2": {
"operator": "lt",
"value": 0.2
},
"M20-nb_usrs": {
"operator": "gte",
"value": 5
},
"M22-rel2raw": {
"operator": "gte",
"value": 0.5
}
"value": 0.5
}
},
"expression": "( ( M1-canonical_ss & M19-mean_mismatches & M20-nb_usrs ) | ( M1-canonical_ss & M12-maxmmes & M11-entropy & M19-mean_mismatches.2 ) | ( M1-canonical_ss.2 & M19-mean_mismatches & M12-maxmmes & M11-entropy ) )"
"expression": "( M4-nb_rel_aln & M12-maxmmes ) | ( M4-nb_rel_aln.2 & M12-maxmmes.2 & M13-hamming5p & M14-hamming3p & M19-mean_mismatches.2 ) | ( M13-hamming5p.2 & M14-hamming3p.2 & M19-mean_mismatches )"
}
77 changes: 77 additions & 0 deletions data/selftrain_initial_pos.layer3.json
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@@ -0,0 +1,77 @@
{
"parameters": {
"M1-canonical_ss": {
"operator": "in",
"value": ["C"]
},
"M1-canonical_ss.2": {
"operator": "in",
"value": ["S"]
},
"M1-canonical_ss.3": {
"operator": "in",
"value": ["N"]
},
"M4-nb_rel_aln": {
"operator": "gte",
"value": 5
},
"M4-nb_rel_aln.2": {
"operator": "gte",
"value": 1
},
"M12-maxmmes": {
"operator": "gte",
"value": 20
},
"M12-maxmmes.2": {
"operator": "gte",
"value": 10
},
"M11-entropy": {
"operator": "gt",
"value": 5.0
},
"M11-entropy.2": {
"operator": "gt",
"value": 2.0
},
"M13-hamming5p": {
"operator": "gte",
"value": 7
},
"M13-hamming5p.2": {
"operator": "gte",
"value": 8
},
"M14-hamming3p": {
"operator": "gte",
"value": 7
},
"M14-hamming3p.2": {
"operator": "gte",
"value": 8
},
"M19-mean_mismatches": {
"operator": "eq",
"value": 0
},
"M19-mean_mismatches": {
"operator": "lt",
"value": 0.1
},
"M20-nb_usrs": {
"operator": "gte",
"value": 5
},
"M22-rel2raw": {
"operator": "gte",
"value": 0.5
},
"M22-rel2raw.2": {
"operator": "gte",
"value": 0.75
}
},
"expression": "( M1-canonical_ss ) | ( M1-canonical_ss.2 & M22-rel2raw & M13-hamming5p & M14-hamming3p ) | ( M1-canonical_ss.3 & M22-rel2raw.2 & M13-hamming5p.2 & M14-hamming3p.2 & M19-mean_mismatches & M11-entropy.2 )"
}
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