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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.

validate

The validate option on the bam executable reads and 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)

convert

The convert option on the bam executable reads a SAM/BAM file and writes it as a SAM/BAM file.

The executable converts the input file into the format of the output file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call:

./bam --in <bamFile>.bam --out <newSamFile>.sam

Don't forget to put in the paths to the executable and your test files.

Parameters

    Required Parameters:
	--in : the SAM/BAM file to be read
	--out : the SAM/BAM file to be written
    Optional Parameters:
	--noeof             : do not expect an EOF block on a bam file.

Usage

./bam convert --in <inputFile> --out <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

dumpHeader

The dumpHeader 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

splitChromosome

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)

writeRegion

The writeRegion option on the bam executable writes the alignments in the indexed BAM file that fall into the specified region (reference id and start/end position).

Parameters

	Required Parameters:
		--in       : the BAM file to be read
		--out      : the SAM/BAM file to write to
	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")
		--refID    : the BAM reference ID to read (defaults to -1: unmapped)
		--start    : the 0-based start position (defaults to -1)
		--end      : the 0-based end position (defaults to -1: meaning til the end of the reference)

Usage

./bam writeRegion --in <inputFilename>  --out <outputFilename> [--bamIndex <bamIndexFile>] [--noeof]

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 [t.sam], --bamIndex [], --refID,
 --start [1], --end [100], --noeof

Wrote t.sam with 2 records.

dumpIndex

The dumpIndex option on the bam executable prints BAM index file in an easy to read format.

Parameters

	Required Parameters:
		bamIndexFile - path/name of the index file to display
	Optional Parameters:
		ref# - the reference number to print (optional) defaults to print all

Usage

./bam dumpIndex <bamIndexFile> <ref#>

Return Value

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

readIndexedBam

The readIndexedBam option on the bam executable reads an indexed BAM file reference id by reference id -1 to 22 and writes it out as a SAM/BAM file.

Parameters

	Required Parameters:
		inputFilename      - path/name of the input BAM file
		outputFile.sam/bam - path/name of the output file
		bamIndexFile       - path/name of the BAM index file
	Optional Parameters:
		ref# - the reference number to print (optional) defaults to print all

Usage

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

Return Value

0

BamUtil

bam Executable

validate

Parameters

Usage

Return Value

Example Output

convert

Parameters

Usage

Return Value

Example Output

dumpHeader

Parameters

Usage

Return Value

Example Output

splitChromosome

Parameters

Usage

Return Value

Example Output

writeRegion

Parameters

Usage

Return Value

Example Output

dumpIndex

Parameters

Usage

Return Value

readIndexedBam

Parameters

Usage

Return Value

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