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uk.ac.* |
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uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean | ||
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public static final java.lang.String |
VALID_RESIDUES |
"ACGTNRYKMBDHV" |
uk.ac.sanger.cgp.standalonecsa.beans.Constants.PreFlagging | ||
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public static final int |
FAIL |
4 |
public static final int |
PASS |
1 |
public static final int |
USEFUL |
2 |
public static final int |
USELESS |
3 |
uk.ac.sanger.cgp.standalonecsa.beans.Constants.TraceStatus | ||
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public static final int |
BAD_AB1_BASE_CALL |
18 |
public static final int |
BAD_COMMENT_BLOCK |
17 |
public static final int |
BAD_TRACE |
11 |
public static final int |
FAILED_MOB_CORR |
13 |
public static final int |
OVERLOADED |
7 |
public static final int |
UNDERLOADED |
6 |
public static final int |
UNKNOWN_CHROMAT_FORMAT |
16 |
uk.ac.sanger.cgp.standalonecsa.beans.Constants.VariantType | ||
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public static final int |
COMPLEX_INDEL |
4 |
public static final int |
DEL |
3 |
public static final int |
GERM_SUB |
10 |
public static final int |
INS |
2 |
public static final int |
REF_SUB |
5 |
public static final int |
SPEC_INDEL |
6 |
public static final int |
SUB |
1 |
public static final int |
TRACE_HOLE |
7 |
uk.ac.sanger.cgp.standalonecsa.beans.Constants.Zygosity | ||
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public static final int |
HETEROZYGOUS |
2 |
public static final int |
HETEROZYGOUS_TO_CHANGE |
3 |
public static final int |
HOMOZYGOUS |
1 |
public static final int |
UNKNOWN |
4 |
uk.ac.sanger.cgp.standalonecsa.util.CsaConfig | ||
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public static final java.lang.String |
CONFIG_LOC |
"standaloneCsa.properties" |
public static final java.lang.String |
CSA_ANALYSIS_LOC |
"./resources/csa_analysis.properties" |
public static final java.lang.String |
DEFAULT_AMPLIMER_CONFIG_LOC |
"amplimer.properties" |
protected static final java.lang.String |
DEFAULT_PROP_LOC |
"/default.properties" |
protected static final java.lang.String |
STATUS_LOC |
"/status.properties" |
uk.ac.sanger.cgp.standalonecsa.util.SetupUtils | ||
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public static final java.lang.String |
ALPHA_NUMERIC |
".*" |
public static final java.lang.String |
CHAR_ONLY |
"^[A-Za-z_\\-]$" |
public static final java.lang.String |
DIGITS_ONLY |
"^[0-9]+$" |
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