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IMPORTANT BUG FIX - Previous version had a bug which reduced sensitivity of portcullis filtering output. This release fixes that. We strongly recommend updating to this version. Fixed a compilation bug that occurs with GCC7. Updated junctools. Now the parser for tabular Portcullis junctions should be more stable, with dynamically calculated indices rather than brittle hard-coded ones
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@@ -49,3 +49,4 @@ callgrind* | |
| /portcullis.files | ||
| /portcullis.includes | ||
| /portcullis.creator.user | ||
| /conftest.cpp | ||
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@@ -4,7 +4,7 @@ | |
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||
| # Autoconf setup | ||
| AC_PREREQ([2.68]) | ||
| AC_INIT([portcullis],[1.1.1],[[email protected]],[portcullis],[http://www.earlham.ac.uk]) | ||
| AC_INIT([portcullis],[1.1.2],[[email protected]],[portcullis],[http://www.earlham.ac.uk]) | ||
| AC_CONFIG_SRCDIR([src/portcullis.cc]) | ||
| AC_CONFIG_AUX_DIR([build-aux]) | ||
| AC_CONFIG_MACRO_DIR([m4]) | ||
|
|
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| @@ -0,0 +1,17 @@ | ||
| { | ||
| "parameters": { | ||
| "maxmmes": { | ||
| "operator": "lt", | ||
| "value": 15 | ||
| }, | ||
| "nb_us_aln": { | ||
| "operator": "lte", | ||
| "value": 1 | ||
| }, | ||
| "rel2raw": { | ||
| "operator": "eq", | ||
| "value": 0 | ||
| } | ||
| }, | ||
| "expression": "( maxmmes & nb_us_aln & rel2raw )" | ||
| } |
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| @@ -0,0 +1,25 @@ | ||
| { | ||
| "parameters": { | ||
| "canonical_ss": { | ||
| "operator": "in", | ||
| "value": ["N", "S"] | ||
| }, | ||
| "rel2raw": { | ||
| "operator": "lt", | ||
| "value": 0.5 | ||
| }, | ||
| "mean_mismatches": { | ||
| "operator": "gte", | ||
| "value": 1 | ||
| }, | ||
| "maxmmes": { | ||
| "operator": "lt", | ||
| "value": 15 | ||
| }, | ||
| "nb_us_aln": { | ||
| "operator": "lte", | ||
| "value": 1 | ||
| } | ||
| }, | ||
| "expression": "( nb_us_aln & maxmmes & rel2raw & ( canonical_ss | mean_mismatches ) )" | ||
| } |
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| @@ -0,0 +1,13 @@ | ||
| { | ||
| "parameters": { | ||
| "canonical_ss": { | ||
| "operator": "in", | ||
| "value": ["N", "S"] | ||
| }, | ||
| "pfp": { | ||
| "operator": "eq", | ||
| "value": 1 | ||
| } | ||
| }, | ||
| "expression": "( canonical_ss & pfp )" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| { | ||
| "parameters": { | ||
| "maxmmes": { | ||
| "operator": "lt", | ||
| "value": 15 | ||
| }, | ||
| "rel2raw": { | ||
| "operator": "lt", | ||
| "value": 0.3 | ||
| } | ||
| }, | ||
| "expression": "( maxmmes & rel2raw )" | ||
| } |
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| @@ -0,0 +1,21 @@ | ||
| { | ||
| "parameters": { | ||
| "nb_rel_aln": { | ||
| "operator": "lt", | ||
| "value": 1 | ||
| }, | ||
| "entropy": { | ||
| "operator": "eq", | ||
| "value": 0 | ||
| }, | ||
| "primary_junc": { | ||
| "operator": "eq", | ||
| "value": 0 | ||
| }, | ||
| "suspicious": { | ||
| "operator": "eq", | ||
| "value": 1 | ||
| } | ||
| }, | ||
| "expression": "( nb_rel_aln & entropy & primary_junc & suspicious )" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| { | ||
| "parameters": { | ||
| "canonical_ss": { | ||
| "operator": "in", | ||
| "value": ["N", "S"] | ||
| }, | ||
| "pfp": { | ||
| "operator": "eq", | ||
| "value": 1 | ||
| } | ||
| }, | ||
| "expression": "( canonical_ss & pfp )" | ||
| } |
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| @@ -0,0 +1,17 @@ | ||
| { | ||
| "parameters": { | ||
| "rel2raw": { | ||
| "operator": "eq", | ||
| "value": 0.0 | ||
| }, | ||
| "hamming5p": { | ||
| "operator": "lte", | ||
| "value": 3 | ||
| }, | ||
| "hamming3p": { | ||
| "operator": "lte", | ||
| "value": 3 | ||
| } | ||
| }, | ||
| "expression": "( rel2raw & hamming5p & hamming3p )" | ||
| } |
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|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| { | ||
| "parameters": { | ||
| "nb_rel_aln": { | ||
| "operator": "gte", | ||
| "value": 1 | ||
| }, | ||
| "maxmmes": { | ||
| "operator": "gte", | ||
| "value": 8 | ||
| }, | ||
| "entropy": { | ||
| "operator": "gt", | ||
| "value": 1.0 | ||
| }, | ||
| "hamming5p": { | ||
| "operator": "gte", | ||
| "value": 4 | ||
| }, | ||
| "hamming3p": { | ||
| "operator": "gte", | ||
| "value": 4 | ||
| }, | ||
| "mean_mismatches": { | ||
| "operator": "lte", | ||
| "value": 1.0 | ||
| }, | ||
| "nb_us_aln": { | ||
| "operator": "gte", | ||
| "value": 1 | ||
| }, | ||
| "rel2raw": { | ||
| "operator": "gte", | ||
| "value": 0.25 | ||
| } | ||
| }, | ||
| "expression": "nb_rel_aln & hamming5p & hamming3p & maxmmes & nb_us_aln & mean_mismatches & rel2raw" | ||
| } |
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| @@ -0,0 +1,45 @@ | ||
| { | ||
| "parameters": { | ||
| "nb_rel_aln.1": { | ||
| "operator": "gte", | ||
| "value": 5 | ||
| }, | ||
| "nb_rel_aln.2": { | ||
| "operator": "gte", | ||
| "value": 3 | ||
| }, | ||
| "maxmmes.1": { | ||
| "operator": "gte", | ||
| "value": 20 | ||
| }, | ||
| "maxmmes.2": { | ||
| "operator": "gt", | ||
| "value": 12 | ||
| }, | ||
| "hamming5p.1": { | ||
| "operator": "gte", | ||
| "value": 7 | ||
| }, | ||
| "hamming5p.2": { | ||
| "operator": "gte", | ||
| "value": 9 | ||
| }, | ||
| "hamming3p.1": { | ||
| "operator": "gte", | ||
| "value": 7 | ||
| }, | ||
| "hamming3p.2": { | ||
| "operator": "gte", | ||
| "value": 9 | ||
| }, | ||
| "mean_mismatches.1": { | ||
| "operator": "lte", | ||
| "value": 0 | ||
| }, | ||
| "mean_mismatches.2": { | ||
| "operator": "lt", | ||
| "value": 0.33 | ||
| } | ||
| }, | ||
| "expression": "( nb_rel_aln.1 & maxmmes.1 ) | ( nb_rel_aln.2 & maxmmes.2 & hamming5p.1 & hamming3p.1 & mean_mismatches.2 ) | ( hamming5p.2 & hamming3p.2 & mean_mismatches.1 )" | ||
| } |
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|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| { | ||
| "parameters": { | ||
| "canonical_ss.1": { | ||
| "operator": "in", | ||
| "value": ["C"] | ||
| }, | ||
| "canonical_ss.2": { | ||
| "operator": "in", | ||
| "value": ["S"] | ||
| }, | ||
| "canonical_ss.3": { | ||
| "operator": "in", | ||
| "value": ["N"] | ||
| }, | ||
| "entropy.1": { | ||
| "operator": "gt", | ||
| "value": 3.0 | ||
| }, | ||
| "entropy.2": { | ||
| "operator": "gt", | ||
| "value": 1.5 | ||
| }, | ||
| "hamming5p.1": { | ||
| "operator": "gte", | ||
| "value": 6 | ||
| }, | ||
| "hamming5p.2": { | ||
| "operator": "gte", | ||
| "value": 7 | ||
| }, | ||
| "hamming3p.1": { | ||
| "operator": "gte", | ||
| "value": 6 | ||
| }, | ||
| "hamming3p.2": { | ||
| "operator": "gte", | ||
| "value": 7 | ||
| }, | ||
| "mean_mismatches.1": { | ||
| "operator": "eq", | ||
| "value": 0 | ||
| }, | ||
| "mean_mismatches.2": { | ||
| "operator": "lt", | ||
| "value": 0.1 | ||
| }, | ||
| "nb_us_aln": { | ||
| "operator": "gte", | ||
| "value": 5 | ||
| }, | ||
| "rel2raw.1": { | ||
| "operator": "gte", | ||
| "value": 0.5 | ||
| }, | ||
| "rel2raw.2": { | ||
| "operator": "gte", | ||
| "value": 0.75 | ||
| }, | ||
| "primary_junc": { | ||
| "operator": "eq", | ||
| "value": 1 | ||
| } | ||
| }, | ||
| "expression": "(( canonical_ss.1 ) | ( canonical_ss.2 & rel2raw.1 & hamming5p.1 & hamming3p.1 ) | ( canonical_ss.3 & rel2raw.2 & hamming5p.2 & hamming3p.2 & mean_mismatches.1 & entropy.2 )) & (primary_junc)" | ||
| } |
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@@ -7,3 +7,4 @@ | |
| /project-config.jam.4 | ||
| *.log | ||
| /project-config.jam.5 | ||
| /project-config.jam.6 | ||
2 changes: 2 additions & 0 deletions
2
deps/boost/libs/config/checks/architecture/bin/gcc-gnu-7/debug/.gitignore
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| @@ -0,0 +1,2 @@ | ||
| /64.o | ||
| /x86.o |
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@@ -9,3 +9,4 @@ config.* | |
| /libtool | ||
| *.la | ||
| /ranger.pc | ||
| /conftest.cpp | ||
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