Difference between revisions of "BamUtil"

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The bam executable has the following functions.
 
The bam executable has the following functions.
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* [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]]
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* [[C++ Executable: bam#validate|validate - Read and Validate a SAM/BAM file]]
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* [[C++ Executable: bam#Read a SAM/BAM file and write as a SAM/BAM file|Read a SAM/BAM file and write as a SAM/BAM file]]
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* [[C++ Executable: bam#convert|convert - Read a SAM/BAM file and write as a SAM/BAM file]]
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* [[C++ Executable: bam#Print SAM/BAM header|Print SAM/BAM header]]
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* [[C++ Executable: bam#dumpHeader|dumpHeader - Print SAM/BAM header]]
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* [[C++ Executable: bam#Split BAM by Chromosome|Split BAM by Chromosome]]
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* [[C++ Executable: bam#splitChromosome|splitChromosome - Split BAM by Chromosome]]
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* [[C++ Executable: bam#Write the alignments in the indexed BAM file that fall into the specified region|Write the alignments in the indexed BAM file that fall into the specified region]]
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* [[C++ Executable: bam#writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region]]
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* [[C++ Executable: bam#Dump a BAM index file|Dump a BAM index file into an easy to read text version]]
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* [[C++ Executable: bam#dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]]
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* [[C++ Executable: bam#Read & Write indexed BAM file|Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file]]
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* [[C++ Executable: bam#readIndexedBam|readIndexedBam - Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file]]
  
 
This executable is built using the [[C++ Library: bam|bam library]].
 
This executable is built using the [[C++ Library: bam|bam library]].

Revision as of 12:01, 30 June 2010

bam Executable

When the pipeline is compiled, the SAM/BAM executable, "bam" is generated in the pipeline/bam/ directory.

The software reads the beginning of an input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension. If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.

The bam executable has the following functions.

This executable is built using the bam library.

Just running ./bam will print the Usage information for the bam executable.


Read and Validate a SAM/BAM file

The validate option on the bam executable validates a SAM/BAM file.

The validation checks that the file is sorted as specified in the user options. Default is unsorted, in which case, no order validation is done.

SAM fields are validated against: SAM Validation Criteria

NOTE: Currently only minimal validation is currently done.

Parameters

    Required Parameters:
	--in : the SAM/BAM file to be validated
    Optional Parameters:
	--noeof             : do not expect an EOF block on a bam file.
	--so_flag           : validate the file is sorted based on the header's @HD SO flag.
	--so_coord          : validate the file is sorted based on the coordinate.
	--so_query          : validate the file is sorted based on the query name.
	--quitAfterErrorNum : Number of records with errors/invalids to allow before quiting.
	                      -1 (default) indicates to not quit until the entire file is validated.
	                      0 indicates not to read/validate anything.
	--maxReportedErrors : Maximum number of errors to print (defaults to 100)

Usage

./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>]

Return Value

  • 0: all records are successfully read, are valid, and are properly sorted.
  • non-0: at least one record was not successfully read, not valid, or not properly sorted.

Example Output

The following parameters are in effect:

Input Parameters
 --in [t.sam], --noeof, --quitAfterErrorNum [-1], --maxReportedErrors [100]
   SortOrder : --so_flag, --so_coord, --so_query

Record 1
FAIL_PARSE: Too few columns in the Record

Record 2
FAIL_PARSE: Too few columns in the Record


Number of records read = 2
Number of valid records = 0
Returning: 5 (FAIL_PARSE)


Read a SAM/BAM file and write as a SAM/BAM file

This executable takes 2/3 arguments. The first argument is the input file. The second argument is the output file. The executable converts the first file into the format of the second file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call: 

./bam <bamFile>.bam <newSamFile>.sam

Don't forget to put in the paths to the executable and your test files. The third argument, NOEOF, specifies that the End-Of-File Block should not be checked for when opening the file.

Usage

./bam <inputFile> <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [NOEOF]

Return Value

Returns the SamStatus for the reads/writes.

Example Output

Number of records read = 10
Number of records written = 10


Print SAM/BAM header

The dump_header option on the bam executable prints the header of the specified SAM/BAM file to cout.

Parameters

    Required Parameters:
	filename : the sam/bam filename whose header should be printed.

Usage

./bam dump_header <inputFile>

Return Value

  • 0: the header was successfully read and printed.
  • non-0: the header was not successfully read or was not printed. (Returns the SamStatus.)


Example Output

@SQ	SN:1	LN:247249719
@SQ	SN:2	LN:242951149
@SQ	SN:3	LN:199501827


Split BAM by Chromosome

The splitChromosome option on the bam executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).

The files all have the same base name, but with an _# where # corresponds with the associated reference id from the BAM file.

Parameters

    Required Parameters:
	--in       : the SAM/BAM file to be split
	--out      : the base filename for the SAM/BAM files to write into.  Does not include the extension.
	             _N will be appended to the basename where N indicates the Chromosome.
    Optional Parameters:
	--noeof  : do not expect an EOF block on a bam file.
	--bamIndex : the path/name of the bam index file
	             (if not specified, uses the --in value + ".bai")
	--bamout : write the output files in BAM format (default).
	--samout : write the output files in SAM format.

Usage

./bam splitChromosome --in <inputFilename>  --out <outputFileBaseName> [--bamIndex <bamIndexFile>] [--noeof] [--bamout|--samout]


Return Value

  • 0: all records are successfully read and written.
  • non-0: at least one record was not successfully read or written.

Example Output

The following parameters are in effect:

Input Parameters
 --in [test/testFiles/sortedBam.bam], --out [chromosome], --bamIndex [],
                 --noeof
   Output Type : --bamout [ON], --samout

Reference ID -1 has 2 records
Reference ID 0 has 5 records
Reference ID 1 has 2 records
Reference ID 2 has 1 records
Reference ID 3 has 0 records
Reference ID 4 has 0 records
Reference ID 5 has 0 records
Reference ID 6 has 0 records
Reference ID 7 has 0 records
Reference ID 8 has 0 records
Reference ID 9 has 0 records
Reference ID 10 has 0 records
Reference ID 11 has 0 records
Reference ID 12 has 0 records
Reference ID 13 has 0 records
Reference ID 14 has 0 records
Reference ID 15 has 0 records
Reference ID 16 has 0 records
Reference ID 17 has 0 records
Reference ID 18 has 0 records
Reference ID 19 has 0 records
Reference ID 20 has 0 records
Reference ID 21 has 0 records
Reference ID 22 has 0 records
Number of records = 10
Returning: 0 (SUCCESS)


Dump a BAM index file

Usage

./bam dump_index <bamIndexFile>

Return Value

  • -1 if the bam index file could not be opened.
  • 0 if the bam index file could be opened.


Read & Write indexed BAM file

Usage

./bam read_indexed_bam <inputFilename> <outputFile.sam/bam> <bamIndexFile>

Return Value

  • 0
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