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BamUtil

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[[Category:Software|BambamUtil]][[Category:libbamC++]]= bam Executable =When the pipeline is compiled, the SAM/BAM executable, "bam" is generated in the pipeline/bam/ directory.[[Category:Software]]
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.= bamUtil Overview =
The bam executable has the following functions.* [[C++ Executable: bam#Read and Validate bamUtil is a repository that contains several programs that perform operations on SAM/BAM file|Read and Validate files. All of these programs are built into a SAM/BAM file]]* [[C++ Executable: single executable, <code>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]]* [[C++ Executable: bam#Print SAM/BAM header|Print SAM/BAM header]]* [[C++ Executable: bam#Split BAM by Chromosome|Split BAM by Chromosome]]* [[C++ Executable: bam#Dump a BAM index file|Dump a BAM index file into an easy to read text version]]* [[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]]code>.
This executable is built using the [[C++ Library: bam|bam library]].
Just running ./bam will print the Usage information for the bam executable.== Getting Help ==
If you have any questions please use the [https://github.com/statgen/bamUtil bamUtil GitHub page] to raise and issue.
== Read and Validate a SAM/BAM file ==See [[BamUtil: FAQ]] to see if your question has already been answered.
The <code>validate</code> option on the bam executable validates a SAM/BAM file. == Where to Find It =={{ToolGitRepo|repoName=bamUtil}}
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.== Releases ==
SAM fields are validated against: [[SAM Validation Criteria]]If you prefer to run the last official release rather than the latest development version, you can download that here.
'''NOTE: Currently only minimal validation is currently doneThere are two versions of the release, one that include libStatGen and one that does not. If you already have libStatGen installed and want to use your own copy, use the version that does not include libStatGen.'''
=== Parameters Full Release (includes libStatGen) ===<pre> 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)</pre>
=== Usage ===To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
For version 1./bam validate --in <inputFile> [--noeof] [--so_flag|--so_coord|--so_query] [--quitAfterErrorNum <numErrors>] [--maxReportedErrors <numReportedErrors>]0.14 and later, please download libStatGen and bamUtil separately:
=== 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 ==='''Version 1.0.14 - Released 7/8/2015'''<pre>*[[LibStatGen Download#Official Releases|libStatGen version 1.0.14]]The following parameters are in effect:*[[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.14]]
Input Parameters
--in [t.sam], --noeof, --quitAfterErrorNum [-1], --maxReportedErrors [100]
SortOrder : --so_flag, --so_coord, --so_query
Record '''Older Releases'''* [[Media:BamUtilLibStatGen.1.0.13.tgz|BamUtilLibStatGen.1.0.13.tgz‎]] - Released 2/20/2015FAIL_PARSE** Contains: Too few columns in the Record[[LibStatGen Download#Official Releases|libStatGen version 1.0.13]] - see link for version updates** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.13]] - see link for version updates
Record 2
FAIL_PARSE: Too few columns in the Record
* [[Media:BamUtilLibStatGen.1.0.12.tar.gz|BamUtilLibStatGen.1.0.12.tgz‎]] - Released 5/14/2014
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.12]] - see link for version updates
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.12]] - see link for version updates
** Adds regions to [[BamUtil: mergeBam|mergeBam]]
** Accept ',' delimiters for the tags string input in [[BamUtil: squeeze|squeeze]], [[BamUtil: revert|revert]], & [[BamUtil: diff|diff]]
Number of records read = *[[Media:BamUtilLibStatGen.1.0.11.tar.gz|BamUtilLibStatGen.1.0.11.tar.gz‎]] - Released 2/28/2014Number of valid records = ** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]] - see link for version updatesReturning** Contains: 5 [[#Release of just BamUtil (FAIL_PARSEdoes not include libStatGen)|bamUtil version 1.0.11]] - see link for version updates</pre>** Now properly supports 'B' & 'f' tags** Cleanup - compile issues
*[[Media:BamUtilLibStatGen.1.0.10.tar.gz|BamUtilLibStatGen.1.0.10.tar.gz‎]] - Released 1/2/2014
** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]] - see link for version updates
** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.10]] - see link for version updates
** Adds PhoneHome/Version checking.
== Read a SAM*[[Media:BamUtilLibStatGen.1.0.9.tgz|BamUtilLibStatGen.1.0.9.tgz‎]] - Released 7/BAM file and write as a SAM7/BAM file ==2013This executable takes 2/3 arguments** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0. The first argument is the input file9]] ** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1. The second argument is the output file0. The executable converts the first file into the format 9]]** Update to [[BamUtil: mergeBam|mergeBam]]*** Update to ignore PG lines with duplicate IDs*** Update to accept merges of the second matching RG lines*** Update to log to stderr if no log/out fileis specified* There is no version 1.0.8. So if you want It was skipped to convert a BAM file to a SAM file, from the pipelinestay in line with libStatGen versions (libStatGen 1.0.8 added vcf support)*[[Media:BamUtilLibStatGen.1.0.7.tgz|BamUtilLibStatGen.1.0.7.tgz‎]] - Released 1/bam29/ directory you just call2013** Contains:[[LibStatGen Download#Official Releases|libStatGen version 1.0.7]] ** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1./bam <bamFile>0.bam <newSamFile>7]]** Update to fix some compile issues on ubuntu 12.sam10Don't forget ** Update use of SamRecord::getStringTag to put in expect the paths return of a const string pointer due to libStatGen v1.0.7 updates** Update SamReferenceInfo usage due to libStatGen v1.0.7 updates** Update to [[BamUtil: diff|diff]]*** Fix DIFF to the executable test and your test filesproperly handle running out of available records. Previously no message was printed when this happened and there was a bug for which file it freed** Update to [[BamUtil: clipOverlap|clipOverlap]]*** Update to facilitate adding other overlap handling functionsThe third argument, <code>NOEOF</code>, specifies ** Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)*** Rename RGMergeBam to MergeBam*** Update to handle files that the End-Of-File Block should not be checked for when opening the file.already have an RG
=== Usage ===*[[Media:BamUtilLibStatGen.1.0.6.tgz|BamUtilLibStatGen.1.0.6.tgz‎]] - Released 11/14/2012 ** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.6]] ** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.6]]** Update to [[BamUtil: trimBam|trimBam]]*** Update to allow trimming a different number of bases from each end of the read*[[Media:BamUtilLibStatGen.1.0.5.tgz|BamUtilLibStatGen.1.0.5.tgz‎]] - Released 10/24/2012** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.5]] ** Contains: [[#Release of just BamUtil (does not include libStatGen)|bamUtil version 1.0.5]]** Updates to: [[BamUtil: dedup|dedup]], [[BamUtil: polishBam|polishBam]], [[BamUtil: recab|recab]]** Update to add compile option to compile without C++0x/bam <inputFile> <outputFileC++11** See [[#Release of just BamUtil (does not include libStatGen)|below]] for additional details on updates*BamUtilLibStatGen.sam1.0.4.tgz‎ - Released skipped*[[Media:BamUtilLibStatGen.1.0.3.tgz|BamUtilLibStatGen.1.0.3.tgz‎]] - Released 09/bam19/ubam 2012** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.3]] ** Contains: [[#Release of just BamUtil (ubam is uncompressed bamdoes not include libStatGen)> |bamUtil version 1.0.3]]** Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]]*[[Media:BamUtilLibStatGen.1.0.2.tgz|BamUtilLibStatGen.1.0.2.tgz‎]] - Released 05/16/2012** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.2]] ** Adds: [[BamUtil: bam2FastQ|bam2FastQ]]*[[Media:BamUtilLibStatGen.1.0.1.tgz|BamUtilLibStatGen.1.0.1.tgz‎]] - Released 05/04/2012** Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.1]] ** Adds: [[BamUtil: splitBam|splitBam]], [[BamUtil: clipOverlap|clipOverlap]], [[BamUtil: trimBam|trimBam]], [[BamUtil: polishBam|polishBam]], [[BamUtil: rgMergeBam|rgMergeBam]], [[BamUtil: gapInfo|gapInfo]]** Adds additional functionality to [[BamUtil: stats|stats]]** Adds leftShifting to [[BamUtil: writeRegion|writeRegion]] and [[BamUtil: convert|convert]]** Adds more diff fields to [[BamUtil: diff|diff]]* [[Media:BamUtilLibStatGen.1.0.0.tgz|BamUtilLibStatGen.1.0.0.tgz‎]] - Released 10/10/2011**Initial release of bamUtil that includes libStatGen version 1.0.0. It started from the tool found in the deprecated StatGen repository.**Contains: [[LibStatGen Download#Official Releases|libStatGen version 1.0.0]] [[BamUtil: validate|validate]], [[BamUtil: convert|convert]], [[BamUtil: dumpHeader|dumpHeader]], [[BamUtil: splitChromosome|splitChromosome]], [[BamUtil: writeRegion|writeRegion]], [[BamUtil: dumpRefInfo|dumpRefInfo]], [[BamUtil: dumpIndex|dumpIndex]], [[BamUtil: readIndexedBam|readIndexedBam]], [[BamUtil: filter|filter]], [[BamUtil: readReference|readReference]], [[BamUtil: revert|revert]], [[BamUtil: diff|diff]], [[BamUtil: squeeze|squeeze]], [[BamUtil: findCigars|findCigars]], [[NOEOFBamUtil: stats|stats]]
=== Return Value Release of just BamUtil (does not include libStatGen) ===Returns the SamStatus for the reads/writes.
=== Example Output ===<pre>Number of records read = 10Number of records written = 10</pre>To install an official release, unpack the downloaded file (tar xvf), cd into the bamUtil_x.x.x directory and type make all.
'''BamUtil.1.0.14 Release Notes'''
* BamUtil Version 1.0.14 - Released 7/8/2015
** https://github.com/statgen/bamUtil/archive/v1.0.14.tar.gz
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.14]]
** Update [[BamUtil: trimBam|trimBam]]
*** Add option to soft clip (-c) instead of trimming
** Update [[BamUtil: clipOverlap|clipOverlap]]
*** Add option to mark reads as unmapped if they are entirely clipped
** Update to [[BamUtil: bam2FastQ|bam2FastQ]]
*** Add option to gzip the output files
*** Add option to split Read Groups into separate fastq files
*** Add option to get the quality from a tag
** Update [[BamUtil: recab|recab]]
*** Update to ignore ref 'N' when building the recalibration table
*** Add ability to bin
** Add Dedup_LowMem tool
== Print SAM'''Older Releases'''* BamUtil Version 1.0.13 - Released 2/BAM header==20/2015The <code>dump_header<** https:/code> option /github.com/statgen/bamUtil/archive/v1.0.13.tar.gz** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.13]]** Makefile Updates*** Improve logic to determine actual path for the library*** Update to append to USER_COMPILE_VARS even if specified on the bam executable prints the header of the specified SAM/BAM command line** Update [[BamUtil: writeRegion|writeRegion]]*** Add option to specify readnames to keep in a file *** Fixed bug that if a read overlapped 2 BED positions, it was printed twice** Update to cout. [[BamUtil: bam2FastQ|bam2FastQ]]*** Update to skip non-primary reads** Update to [[BamUtil: polishBam|polishBam]]*** Update to handle '\t' string inputs and to add CO option*** Fix MD5sum calculation to convert fasta to uppercase prior to calculating
=== Parameters ===* [[Media:BamUtil.1.0.12.tgz|BamUtil.1.0.12.tgz‎]] - Released 5/14/2014<pre>** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.12]] Required Parameters** Update [[BamUtil:mergeBam|mergeBam]]*** Add a regions option filename ** Update to [[BamUtil: squeeze|squeeze]], [[BamUtil: revert|revert]], [[BamUtil: diff|diff]]*** Also accept ',' instead of just ';' as the sam/bam filename whose header should be printeddelimiter in the input tags string.</pre>
=== Usage ===* [[Media:BamUtil.1.0.11.tgz|BamUtil.1.0.11.tgz‎]] - Released 2/28/2014** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.11]]*** Adds support for 'B' & 'f' tags that did not work properly before.** Update [[BamUtil: splitBam|splitBam]] & [[BamUtil: polishBam|polishBam]]*** Update to work properly if log & output file are not specified (no longer creates '.log')** Update Main dummy/example tool to indicate the correct tool** Update to [[BamUtil: bam2FastQ|bam2FastQ]], [[BamUtil: clipOverlap|clipOverlap]], [[BamUtil: filter|filter]], [[BamUtil: mergeBam|mergeBam]], [[BamUtil: splitBam|splitBam]], [[BamUtil: squeeze|squeeze]], [[BamUtil: stats|stats]]*** Cleanup usage/parameter descriptions** Update [[BamUtil: revert|revert]]*** Update compatibility with libStatGen due to 'B' & 'f' tag handling updates** Add tests for 'B' & 'f' tags
* [[Media:BamUtil.1.0.10.tar.gz|BamUtil.1.0.10.tar.gz‎]] - Released 1/2/bam dump_header <inputFile>2014** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.10]]** All*** Add PhoneHome/version checking*** Make sub-program names case independent*** Fix Logger.cpp compiler warning** Adds: [[BamUtil: explainFlags|explainFlags]] - describes the SAM/BAM flags based on the flag value** Update to [[BamUtil: stats|stats]]*** Fix Stats to not try to not try to process a record after it is out of the loop (it would already have been processed or is invalid)** Update to [[BamUtil: splitBam|splitBam]]*** fix description of --noeof option** Update to [[BamUtil: writeRegion|writeRegion]]*** add exclude/required flags** Update to [[BamUtil: dedup|dedup]] & [[BamUtil: recab|recab]]*** Ignore secondary reads for dedup and making the recalibration table.*** skip QC Failures*** add excludeFlags parameters** Update to [[BamUtil: clipOverlap|clipOverlap]]*** add exclude flags*** fix bug for readName sorted when a read is filtered due to flags*** add sorting validation** Update to [[BamUtil: bam2FastQ|bam2FastQ]]*** add --merge option to generate interleaved files.*** update to open the input file before opening the output files, so if there is an error, the outputs aren't opened** Update to [[BamUtil: mergeBam|mergeBam]]*** add option to ignore the RG PI field when checking headers*** add more informative header merge error messages
=== Return Value ===* [[Media:BamUtil.1.0.9.tgz|BamUtil.1.0: the header was successfully read and printed.9.tgz‎]] - Released 7/7/2013* non-* Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0: the header was not successfully read or was not printed. 9]] (Returns the SamStatusversion 1.0.7 should also work)** Update to [[BamUtil: mergeBam|mergeBam]]*** Update to ignore PG lines with duplicate IDs*** Update to accept merges of matching RG lines*** Update to log to stderr if no log/out file is specified
*[[Media:BamUtil.1.0.7.tgz|BamUtil.1.0.7.tgz‎]] - Released 1/29/2013
** Requires, but does not include: [[LibStatGen Download#Official Releases|libStatGen version 1.0.7]] or above
** Update to fix some compile issues on ubuntu 12.10
** Update use of SamRecord::getStringTag to expect the return of a const string pointer due to libStatGen v1.0.7 updates
** Update SamReferenceInfo usage due to libStatGen v1.0.7 updates
** Update to [[BamUtil: diff|diff]]
*** Fix DIFF to test and properly handle running out of available records. Previously no message was printed when this happened and there was a bug for which file it freed
** Update to [[BamUtil: clipOverlap|clipOverlap]]
*** Update to facilitate adding other overlap handling functions
** Update to [[BamUtil: mergeBam|mergeBam]] (formerly RGMergeBam)
*** Rename RGMergeBam to MergeBam
*** Update to handle files that already have an RG
*[[Media:BamUtil.1.0.6.tgz|BamUtil.1.0.6.tgz‎]] - Released 11/14/2012
** Update to [[BamUtil: trimBam|trimBam]]
*** Update to allow trimming a different number of bases from each end of the read
*[[Media:BamUtil.1.0.5.tgz|BamUtil.1.0.5.tgz‎]] - Released 10/24/2012
** Update to [[BamUtil: dedup|dedup]]
*** Update logic for which pair to keep if they have the same quality
** Update to [[BamUtil: polishBam|polishBam]]
*** Update to print the number of successful header additions
** Update to [[BamUtil: recab|recab]]
*** Update to print the number of base skipped due to the base quality
** General Updates
*** Update to add compile option to compile without C++0x/C++11
*BamUtil.1.0.4.tgz‎ - Released skipped
*[[Media:BamUtil.1.0.3.tgz|BamUtil.1.0.3.tgz‎]] - Released 09/19/2012
** Adds: [[BamUtil: dedup|dedup]] [[BamUtil: recab|recab]]
** General Updates
*** Update Logger to write to stderr if output is stdout
** Update to [[BamUtil: stats|stats]]
*** Add required/exclude flags
*** Exclude Clips if excluding umapped
*** Add --withinRegion flag
*** Update phred/qual counts to be uint64_t instead of int to avoid overflow
** Update to [[BamUtil: validate|validate]]
*** Detect header failures
** Update to [[BamUtil: diff|diff]]
*** Update to specify chromosome/pos in ZP as a string rather than int so both can be shown
** Update to [[BamUtil: readReference|readReference]]
*** Output error message if the reference name is not found
** Update to [[BamUtil: splitChromosome|splitChromosome]]
*** Update to actually split the chromosomes and not just hard coded to output chromosomes ids 0-22
** Update Makefile to have cloneLib for cloning libStatGen
*[[Media:BamUtil.1.0.2.tgz|BamUtil.1.0.2.tgz‎]] - Released 05/16/2012
** Adds: [[BamUtil: bam2FastQ|bam2FastQ]]
*[[Media:BamUtil.1.0.1.tgz|BamUtil.1.0.1.tgz‎]] - Released 05/04/2012
** Adds: [[BamUtil: splitBam|splitBam]], [[BamUtil: clipOverlap|clipOverlap]], [[BamUtil: trimBam|trimBam]], [[BamUtil: polishBam|polishBam]], [[BamUtil: rgMergeBam|rgMergeBam]], [[BamUtil: gapInfo|gapInfo]]
** Adds additional functionality to [[BamUtil: stats|stats]]
** Adds leftShifting to [[BamUtil: writeRegion|writeRegion]] and [[BamUtil: convert|convert]]
** Adds more diff fields to [[BamUtil: diff|diff]]
*[[Media:BamUtil.1.0.0.tgz|BamUtil.1.0.0.tgz‎]] - Released 10/10/2011
**Initial release of just bamUtil. It started from the tool found in the deprecated StatGen repository.
**Contains: [[BamUtil: validate|validate]], [[BamUtil: convert|convert]], [[BamUtil: dumpHeader|dumpHeader]], [[BamUtil: splitChromosome|splitChromosome]], [[BamUtil: writeRegion|writeRegion]], [[BamUtil: dumpRefInfo|dumpRefInfo]], [[BamUtil: dumpIndex|dumpIndex]], [[BamUtil: readIndexedBam|readIndexedBam]], [[BamUtil: filter|filter]], [[BamUtil: readReference|readReference]], [[BamUtil: revert|revert]], [[BamUtil: diff|diff]], [[BamUtil: squeeze|squeeze]], [[BamUtil: findCigars|findCigars]], [[BamUtil: stats|stats]]
=== Example Output =Citation ==<pre>@SQ SNIf you use BamUtil, please cite our publication on GotCloud which includes BamUtil:1 LN:247249719@SQ SN[http:2 LN:242951149@SQ SN:3 LN//genome.cshlp.org/content/early/2015/04/14/gr.176552.114.abstract Jun, Goo, et al. "An efficient and scalable analysis framework for variant extraction and refinement from population scale DNA sequence data." Genome research (2015):199501827</pre>gr-176552.]
== Split BAM by Chromosome =Programs =
The <code>splitChromosome</code> option on software reads the bam executable splits beginning of 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 ===<pre> Required Parameters: --in : the SAM/BAM input file to be split --out : the base filename for the determine if it is SAM/BAM files to write into. Does not include To determine 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 pathformat (SAM/name BAM) of the bam index output file (if not specified, uses the --in value + ".bai") --bamout : write software checks the output files in BAM format (default)file's extension. --samout : write If the output files in SAM formatextension is ".</pre> === 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 ===<pre>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 recordsReference ID 0 has 5 recordsReference ID 1 has 2 recordsReference ID 2 has 1 recordsReference ID 3 has 0 recordsReference ID 4 has 0 recordsReference ID 5 has 0 recordsReference ID 6 has 0 recordsReference ID 7 has 0 recordsReference ID 8 has 0 recordsReference ID 9 has 0 recordsReference ID 10 has 0 recordsReference ID 11 has 0 recordsReference ID 12 has 0 recordsReference ID 13 has 0 recordsReference ID 14 has 0 recordsReference ID 15 has 0 recordsReference ID 16 has 0 recordsReference ID 17 has 0 recordsReference ID 18 has 0 recordsReference ID 19 has 0 recordsReference ID 20 has 0 recordsReference ID 21 has 0 recordsReference ID 22 has 0 recordsNumber of records = 10Returning: 0 (SUCCESS)</pre>  == Dump " it writes a BAM index file == === Usage === ./bam dump_index <bamIndexFile> === Return Value ===* -1 if the bam index , otherwise it writes a SAM 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{{BamUtilPrograms}}

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