SamFileFormatException: Sam format exceptions

Description Usage Arguments Value Functions Htsjdk Exceptions See Also

View source: R/SamExceptions.R

Description

These are a collection of functions to create data exception objects when there are problems with the format or content of sam files or sam data.

Usage

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SamFileFormatException(path = NA, line = NA, data = NA,
  message = "*", call = NULL, package = packageName(), ...)

SamFileHeaderException(path = NA, line = NA, data = NA,
  message = "*", call = NULL, package = packageName(), ...)

SamFileReadException(path = NA, line = NA, data = NA,
  message = "*", call = NULL, package = packageName(), ...)

MISSING_HEADER_Exception(path = NA, data = NA, line = NA,
  message = "*", call = NULL, package = packageName(), ...)

HeaderOnlyException(path = NA, data = NA, line = NA, message = "*",
  call = NULL, package = packageName(), ...)

Arguments

path

The path associated with an exception, as a one element character vector. It may be NA but should not be NULL. Accessible via the the exceptionPath S3 accessor.

line

The line number associated with an exception, as a one element integer vector. It may be NA but should not be NULL. Accessible via the the exceptionLine S3 accessor.

data

The data or value associated with an exception, the format can vary. Accessible via the the exceptionData S3 accessor.

message

The message associated with the exception, for reading by humans. The default message is usually good enough, but can be overridden through this parameter if needed. When constructed inside packages, the message displayed will have the name of the package prepended as '[package] message' due to conditionMessage being over-ridden for Exception subclasses.

call

The call or call stack associated with the exception. By default this is NULL as IOExceptions are usually environment problems. Can be overridden to provide the sys.calls call stack or a single sys.call.

package

The package where this exception is generated. May be NULL when exceptions are generated and signaled from interactive or script level code and not from a package. Attempts to guess the package by default. Will usually include the package in the displayed message.

...

Extra parameters for additional key=value data as desired.

Value

An Exception object whose class hierarchy is set by the function call and that may contain additional data.

Functions

Htsjdk Exceptions

Names in all capitals are consistent with Htsjdk Exceptions (A Java API for high-throughput sequencing data (HTS) formats, https://github.com/samtools/htsjdk, specifically the MIT licensed file ‘src/main/java/htsjdk/samtools/SAMValidationError.java’). These Java errors are used, for instance, by then MIT licensed Picard tools, http://broadinstitute.github.io/picard/

See Also

Exception


jefferys/SamSeq documentation built on Oct. 25, 2019, 8:11 a.m.