Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DETAIL_FILE_EXTENSION |
"rrbs_detail_metrics" |
public static final String |
PDF_FILE_EXTENSION |
"rrbs_qc.pdf" |
public static final String |
SUMMARY_FILE_EXTENSION |
"rrbs_summary_metrics" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BAIT_BIAS_DETAILS_EXT |
".bait_bias_detail_metrics" |
public static final String |
BAIT_BIAS_SUMMARY_EXT |
".bait_bias_summary_metrics" |
public static final String |
PRE_ADAPTER_DETAILS_EXT |
".pre_adapter_detail_metrics" |
public static final String |
PRE_ADAPTER_SUMMARY_EXT |
".pre_adapter_summary_metrics" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
USAGE |
"Generate a SAM or BAM file from data in an Illumina basecalls output directory" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
MASKING_QUALITY |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final boolean |
DefaultSkipEmptyFiles |
true |
public static final String |
PER_TILE_PATTERN_STRING |
"s_(\\d+)_(\\d{1,5})" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
PARAMETER_DOC |
"A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of \"36T8B8S28T\" then, before being converted to SAM records those bases will be split into 4 reads where read one consists of 36 cycles of template, read two consists of 8 cycles of barcode, read three will be an 8 base read of skipped cycles and read four is another 28 cycle template read. The read consisting of skipped cycles would NOT be included in output SAM/BAM file read groups." |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
MAX_POS |
1.0E7f |
public static final float |
MIN_POS |
-10.0f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ILLUMINA_ALLEGED_MINIMUM_QUALITY |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public final int |
EXPECTED_VERSION |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
detailedMetricsExtension |
".pffail_detailed_metrics" |
public static final String |
summaryMetricsExtension |
".pffail_summary_metrics" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
UNKNOWN |
"unknown" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_RECORDS_IN_RAM |
500000 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
NO_LIBRARIES_SPECIFIED_IN_HEADER |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_OPTICAL_DUPLICATE_DISTANCE |
100 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final byte |
F |
0 |
public static final byte |
FF |
2 |
public static final byte |
FR |
3 |
public static final byte |
R |
1 |
public static final byte |
RF |
5 |
public static final byte |
RR |
4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
SIZE_OF |
65 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DEFAULT_READ_NAME_REGEX |
"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_ADAPTER_LENGTH |
30 |
public static final int |
DEFAULT_NUM_ADAPTERS_TO_KEEP |
1 |
public static final int |
DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN |
100 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_QUEUE_SIZE |
2000 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MAX_ERROR_RATE |
0.1 |
public static final double |
MAX_PE_ERROR_RATE |
0.1 |
public static final int |
MIN_MATCH_BASES |
12 |
public static final int |
MIN_MATCH_PE_BASES |
6 |
public static final int |
NO_MATCH |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
BARCODE_DELIMITER |
"-" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MAX_PROB_BELOW_ONE |
0.9999999999999999 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
CONTINGENCY_METRICS_FILE_EXTENSION |
".genotype_concordance_contingency_metrics" |
public static final String |
DETAILED_METRICS_FILE_EXTENSION |
".genotype_concordance_detail_metrics" |
public static final String |
SUMMARY_METRICS_FILE_EXTENSION |
".genotype_concordance_summary_metrics" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FILTER_CANNOT_LIFTOVER |
"FailedLiftover" |
public static final String |
FILTER_MISMATCHING_REF_ALLELE |
"MismatchedRefAllele" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
AB_FILTER |
"AlleleBalance" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ALL_GTS_FILTERED |
"AllGtsFiltered" |
public static final String |
PASS_FILTER |
"PASS" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FILTER_NAME |
"LowQD" |