SamFileFormatException: Sam format exceptions

In jefferys/SamSeq: Work with aligned reads from a SAM file

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

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

• SamFileFormatException: This exception and sub-classes describe problems with sam files.

  • message = [package] A SamFileFormatException occurred at line line in sam file: "file". (Running in: "getwd()"). That line began: "first 80 char of data".

  • class = c( "SamFileFormatException", "FileFormatException", "DataException", "Exception", "condition" )

• SamFileHeaderException: This exception and sub-classes describe problems with sam file headers.

  • message = [package] A SamFileHeaderException occurred parsing the sam file header at line line in file: "file". (Running in: "getwd()"). That line began: "first 80 char of data".

  • class = c( "SamFileHeaderException", "SamFileFormatException", "FileFormatException", "DataException", "Exception", "condition" )

• SamFileReadException: This exception and sub-classes describe problems with sam file reads.

  • message = [package] A SamFileReadException occurred parsing the sam file read at line line in file: "file". (Running in: "getwd()"). That line began: "first 80 char of data".

  • class = c( "SamFileReadException","SamFileFormatException", "FileFormatException", "DataException", "Exception", "condition" )

• MISSING_HEADER_Exception: Sam files require headers. Temporary files with just reads are not true sam files.

  • message = [package] A MISSING_HEADER Exception occurred in sam file: "file". (Running in: "getwd()"). Sam files require headers. Temporary files with just reads are not true sam files.'

  • class = c( "MISSING_HEADER_Exception", "SamFileHeaderException", "SamFileFormatException", "FileFormatException", "DataException", "Exception", "condition" )

• HeaderOnlyException: Sam files require reads. Temporary files with just headers are not true sam files.

  • message = [package] A HeaderOnlyException occurred in sam file: "file". (Running in: "getwd()"). Sam files require reads. Temporary files with just headers are not true sam files.'

  • class = c( "HeaderOnlyException", "SamFileReadException", "SamFileFormatException", "FileFormatException", "DataException", "Exception", "condition" )

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.