Template:OutBAMOutputFile - Revision history

Mktrost at 20:56, 6 January 2014

2014-01-06T20:56:08Z

← Older revision		Revision as of 16:56, 6 January 2014
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	{{{hdr\|===}}} ~~output~~ File (<code>--out</code>) {{{hdr\|===}}}		{{{hdr\|===}}} Output File ({{#if: {{{noParam\|}}} \| {{{noParam}}} argument\|<code>{{{param\|--out}}}</code>}}) {{{hdr\|===}}}

	Use <code>--out</code> followed by your file name to specify the SAM/BAM output file.		{{#if: {{{noParam\|}}} \| The {{{noParam}}} argument is the name of the output SAM/BAM file. \|
			Use <code>{{{param\|--out}}}</code> followed by your file name to specify the SAM/BAM output file.}}

	The file extension is used to determine whether to write SAM/BAM/uncompressed BAM. A <code>-</code> is used to indicate stdout and the extension for file type (no extension is SAM).		The file extension is used to determine whether to write SAM/BAM/uncompressed BAM. A <code>-</code> is used to indicate stdout and the extension for file type (no extension is SAM).
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	{\|border="1" cellspacing="0" cellpadding="2"		{\|border="1" cellspacing="0" cellpadding="2"
	\|SAM to file		\|SAM to file
	\| <code>--out yourFileName.sam</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--out}} yourFileName.sam</code>
	\|-		\|-
	\|BAM to file		\|BAM to file
	\| <code>--out yourFileName.bam</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--out}} yourFileName.bam</code>
	\|-		\|-
	\|Uncompressed BAM to file		\|Uncompressed BAM to file
	\| <code>--out yourFileName.ubam</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--out}} yourFileName.ubam</code>
	\|-		\|-
	\|SAM to stdout		\|SAM to stdout
	\| <code>--out -</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--out}} -</code>
	\|-		\|-
	\|BAM to stdout		\|BAM to stdout
	\| <code>--out -.bam</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--out}} -.bam</code>
	\|-		\|-
	\|Uncompressed BAM to stdout		\|Uncompressed BAM to stdout
	\| <code>--out -.ubam</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--out}} -.ubam</code>
	\|}		\|}


	Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.		Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.

Mktrost at 21:36, 3 January 2014

2014-01-03T21:36:36Z

← Older revision		Revision as of 17:36, 3 January 2014
Line 1:		Line 1:
	{{{hdr\|==}}} output File (<code>--out</code>) {{{hdr\|==}}}		{{{hdr\|===}}} output File (<code>--out</code>) {{{hdr\|===}}}

	Use <code>--out</code> followed by your file name to specify the SAM/BAM output file.		Use <code>--out</code> followed by your file name to specify the SAM/BAM output file.

Mktrost at 21:26, 3 January 2014

2014-01-03T21:26:40Z

← Older revision		Revision as of 17:26, 3 January 2014
Line 1:		Line 1:
	== output File (<code>--out</code>) ==		{{{hdr\|==}}} output File (<code>--out</code>) {{{hdr\|==}}}

	Use <code>--out</code> followed by your file name to specify the SAM/BAM output file.		Use <code>--out</code> followed by your file name to specify the SAM/BAM output file.

Mktrost: --out BAM Output File

2011-10-07T13:26:34Z

--out BAM Output File

New page

== output File (<code>--out</code>) ==

Use <code>--out</code> followed by your file name to specify the SAM/BAM output file.

The file extension is used to determine whether to write SAM/BAM/uncompressed BAM. A <code>-</code> is used to indicate stdout and the extension for file type (no extension is SAM).

{|border="1" cellspacing="0" cellpadding="2"
|SAM to file
| <code>--out yourFileName.sam</code>
|-
|BAM to file
| <code>--out yourFileName.bam</code>
|-
|Uncompressed BAM to file
| <code>--out yourFileName.ubam</code>
|-
|SAM to stdout
| <code>--out -</code>
|-
|BAM to stdout
| <code>--out -.bam</code>
|-
|Uncompressed BAM to stdout
| <code>--out -.ubam</code>
|}

Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.