Package | Description |
---|---|
biolockj.module | |
biolockj.module.implicit |
The modules in this package are implicitly added to pipelines as needed.
These modules cannot be directly added to any pipeline unless overridden via pipeline.disableImplicitModules=Y. |
biolockj.module.seq |
BioModule s used to prepare sequence files or update the metadata prior to classification. |
biolockj.util |
Static utilities centralize and organize reusable core methods.
|
Modifier and Type | Method and Description |
---|---|
List<File> |
SeqModuleImpl.getSeqFiles(Collection<File> files) |
List<File> |
SeqModule.getSeqFiles(Collection<File> files)
Return only sequence files for sample IDs found in the metadata file.
If Config ."metadata.required" = "Y", an
error is thrown to list the files that cannot be matched to a metadata row. |
Modifier and Type | Method and Description |
---|---|
List<File> |
Demultiplexer.getSeqFiles(Collection<File> files) |
List<File> |
RegisterNumReads.getSeqFiles(Collection<File> files) |
Modifier and Type | Method and Description |
---|---|
List<File> |
RarefySeqs.getSeqFiles(Collection<File> files) |
List<File> |
Multiplexer.getSeqFiles(Collection<File> files) |
List<File> |
TrimPrimers.getSeqFiles(Collection<File> files) |
List<File> |
AwkFastaConverter.getSeqFiles(Collection<File> files) |
List<File> |
SeqFileValidator.getSeqFiles(Collection<File> files) |
Modifier and Type | Method and Description |
---|---|
static String |
SeqUtil.getSampleId(File file) |
static List<File> |
SeqUtil.getSeqFiles(Collection<File> files)
Return only sequence files for sample IDs found in the metadata file.
If Config ."metadata.required" = "Y", an
error is thrown to list the files that cannot be matched to a metadata row. |