Mktrost: Created page with "explainFlags Category:BAM Software Category:Software = Overview of the `explainFlags` function of `bamUtil` = The `exp..."`


2014-01-06T23:01:39Z
Created page with "explainFlags Category:BAM Software Category:Software  = Overview of the <code>explainFlags</code> function of <code>bamUtil</code> = The <code>exp..."
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[[Category:BamUtil|explainFlags]]

[[Category:BAM Software]]

[[Category:Software]]



= Overview of the <code>explainFlags</code> function of <code>bamUtil</code> =

The <code>explainFlags</code> option on the [[bamUtil]] executable prints a text description of the specified flag value.



This function was added in version 1.0.10.



= Usage =

 ./bam explainFlags --hex|dec <flag> [--params]



= Parameters =

<pre>

	FlagValue Parameters:

		--hex     : Explain this hex flag

		--dec     : Explain this decimal flag

		--params  : print the parameter settings

</pre>

{{PhoneHomeParamDesc}}



== Required Parameters ==

=== Flag Value (<code>--hex</code>, <code>--dec</code>) ===

The flag to translate to text can be either a decimal integer or a hex number.



Use <code>--dec</code> to translate a decimal integer.



Use <code>--hex</code> to translate a hex number.  The hex number can be specified with or without the preceding "0x", producing the same result either way.



==Optional Parameters ==

{{paramsParameter}}



{{PhoneHomeParameters}}



= Return Value =

0 on success, non-0 on error.



= Example Output =

== bin/bam explainFlags --hex 0x70C==

<pre>

0x70c (1804):

	unmapped

	mate unmapped

	unknown fragment

	secondary alignment

	fails QC checks

	duplicate



Number of records read = 10

Number of records written = 10

</pre>



== bin/bam explainFlags --hex 704==

<pre>

0x704 (1796):

	unmapped

	unknown fragment

	secondary alignment

	fails QC checks

	duplicate

</pre>



== bin/bam explainFlags --dec 1804==

<pre>

0x70c (1804):

	unmapped

	mate unmapped

	unknown fragment

	secondary alignment

	fails QC checks

	duplicate

</pre>

BamUtil: explainFlags - Revision history

Mktrost: Created page with "explainFlags Category:BAM Software Category:Software = Overview of the explainFlags function of bamUtil = The exp..."

Mktrost: Created page with "explainFlags Category:BAM Software Category:Software = Overview of the `explainFlags` function of `bamUtil` = The `exp..."`