Top Level Namespace
- Includes:
- RecoverMid, Term::ANSIColor
Defined Under Namespace
Modules: JsonUtils, RecoverMid, Seqtrimnext Classes: ActionAbAdapter, ActionAbFarAdapter, ActionAbLeftAdapter, ActionEmptyInsert, ActionIgnoreRepeated, ActionIndetermination, ActionInducedLowComplexity, ActionInsert, ActionIsContaminated, ActionKey, ActionLeftAdapter, ActionLeftPrimer, ActionLinker, ActionLowComplexity, ActionLowHighSize, ActionLowQuality, ActionManager, ActionMid, ActionMiddleAdapter, ActionMultipleLinker, ActionPairedReads, ActionPolyA, ActionPolyT, ActionRemAditArtifacts, ActionRightAdapter, ActionRightPrimer, ActionSangerLeftAdapter, ActionSangerRightAdapter, ActionShortInsert, ActionTrim, ActionUnexpectedPolyT, ActionUnexpectedVector, ActionUserContaminant, ActionVectors, Array, ExtractSamples, ExtractStats, FastaProcessor, File, GMatch, GnuPlotGraph, GraphStats, Hash, InstallDatabase, InstallRequirements, ListDb, LoadFastaNamesInHash, LoadQualInHash, MakeBlastDb, OneBlast, Params, Piro, Plugin, PluginAbAdapters, PluginAdapters, PluginAdaptersOld, PluginAmplicons, PluginContaminants, PluginExtractInserts, PluginFindPolyAt, PluginIgnoreRepeated, PluginIndeterminations, PluginKey, PluginLinker, PluginLowComplexity, PluginLowHighSize, PluginLowQuality, PluginManager, PluginMids, PluginRemAditArtifacts, PluginSangerAdapters, PluginShortInsert, PluginSizeTrim, PluginUserContaminants, PluginVectors, Regexp, ScanForRestrSite, ScbiStats, Seqtrim, SeqtrimAction, SeqtrimWorkManager, SeqtrimWorker, Sequence, SequenceGroup, SequenceWithAction, String
Constant Summary collapse
- ROOT_PATH =
File.join(File.dirname(__FILE__),'seqtrimnext')
- MAX_POLY_T_FROM_LEFT =
MAX_RUBBISH = 3
4- MIN_TN_COUNT =
15- MAX_POLY_A_FROM_RIGHT =
10- MIN_MIDDLE_POLY_A_SIZE =
35- MIN_MIDDLE_POLY_T_SIZE =
35- MAX_DUST_DISTANCE_FROM_POLYT =
30- MIN_DUST_SIZE =
30- OUTPUT_PATH =
'output_files'- STATS_PATH =
OUTPUT_PATH=‘output_files’
File.join(OUTPUT_PATH,'stats.json')