Template:InBAMInputFile - Revision history

Mktrost at 02:31, 9 April 2019

2019-04-09T02:31:23Z

← Older revision		Revision as of 22:31, 8 April 2019
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	The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|}}} \|.\|, unless your input file is stdin.}}		The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|}}} \|.\|, unless your input file is stdin.}}

	{{#if: {{{noStdin\|}}}\|This tool does not support input from stdin.\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}		{{#if: {{{noStdin\|}}}\|Note: This tool does not support input from stdin.\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}

	{\|border="1" cellspacing="0" cellpadding="2"		{\|border="1" cellspacing="0" cellpadding="2"

Mktrost at 02:30, 9 April 2019

2019-04-09T02:30:41Z

← Older revision		Revision as of 22:30, 8 April 2019
Line 4:		Line 4:
	Use <code>{{{param\|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}		Use <code>{{{param\|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}

	The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|}}} .\|, unless your input file is stdin.}}		The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|}}} \|.\|, unless your input file is stdin.}}

	{{#if: {{{noStdin\|}}}\|This tool does not support input from stdin.\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}		{{#if: {{{noStdin\|}}}\|This tool does not support input from stdin.\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}

Mktrost at 02:29, 9 April 2019

2019-04-09T02:29:34Z

Mktrost at 02:19, 9 April 2019

2019-04-09T02:19:06Z

← Older revision		Revision as of 22:19, 8 April 2019
Line 13:		Line 13:
	\|-		\|-
	\|{{#if: {{{noStdin\|}}} \| \|SAM from stdin}}		\|{{#if: {{{noStdin\|}}} \| \|SAM from stdin}}
	\| <code>{{#if: {{{noParam\|}}} \| \|--in}} -</code>		\|{{#if: {{{noStdin\|}}} \| \|<code>{{#if: {{{noParam\|}}} \| \|--in}} -</code>}}
	\|-		\|-
	\|BAM from stdin		\|BAM from stdin

Mktrost at 02:17, 9 April 2019

2019-04-09T02:17:30Z

← Older revision		Revision as of 22:17, 8 April 2019
Line 4:		Line 4:
	Use <code>{{{param\|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}		Use <code>{{{param\|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}

	The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.		The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|.}}}\|, unless your input file is stdin.}}

	A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).		{{#if: {{{noStdin\|This tool does not support input from stdin.}}}\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}

	{\|border="1" cellspacing="0" cellpadding="2"		{\|border="1" cellspacing="0" cellpadding="2"
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	\| <code>{{#if: {{{noParam\|}}} \| \|--in}} yourFileName</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--in}} yourFileName</code>
	\|-		\|-
	\|SAM from stdin		\|{{#if: {{{noStdin\|}}} \| \|SAM from stdin}}
	\| <code>{{#if: {{{noParam\|}}} \| \|--in}} -</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--in}} -</code>
	\|-		\|-

Mktrost at 20:53, 6 January 2014

2014-01-06T20:53:19Z

← Older revision		Revision as of 16:53, 6 January 2014
Line 1:		Line 1:
	{{{hdr\|===}}} Input File ({{#if: {{{noParam\|}}} \| {{{noParam}}} ~~Parameter~~\|<code>{{{param\|--in}}}</code>}}) {{{hdr\|===}}}		{{{hdr\|===}}} Input File ({{#if: {{{noParam\|}}} \| {{{noParam}}} argument\|<code>{{{param\|--in}}}</code>}}) {{{hdr\|===}}}

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

Mktrost at 20:49, 6 January 2014

2014-01-06T20:49:00Z

← Older revision		Revision as of 16:49, 6 January 2014
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	{{{hdr\|===}}} ~~input~~ File (<code>--in</code>) {{{hdr\|===}}}		{{{hdr\|===}}} Input File ({{#if: {{{noParam\|}}} \| {{{noParam}}} Parameter\|<code>{{{param\|--in}}}</code>}}) {{{hdr\|===}}}

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

	The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.		The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
Line 9:		Line 10:
	{\|border="1" cellspacing="0" cellpadding="2"		{\|border="1" cellspacing="0" cellpadding="2"
	\|SAM/BAM/Uncompressed BAM from file		\|SAM/BAM/Uncompressed BAM from file
	\| <code>--in yourFileName</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--in}} yourFileName</code>
	\|-		\|-
	\|SAM from stdin		\|SAM from stdin
	\| <code>--in -</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--in}} -</code>
	\|-		\|-
	\|BAM from stdin		\|BAM from stdin
	\| <code>--in -.bam</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--in}} -.bam</code>
	\|-		\|-
	\|Uncompressed BAM from stdin		\|Uncompressed BAM from stdin
	\| <code>--in -.ubam</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--in}} -.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

2014-01-03T21:36:00Z

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

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

Mktrost at 21:25, 3 January 2014

2014-01-03T21:25:55Z

← Older revision		Revision as of 17:25, 3 January 2014
Line 1:		Line 1:
	== input File (<code>--in</code>) ==		{{{hdr\|==}}} input File (<code>--in</code>) {{{hdr\|==}}}

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

Mktrost: --in BAM InputFile Template

2011-10-07T13:25:46Z

--in BAM InputFile Template

New page

== input File (<code>--in</code>) ==

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

The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.

A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).

{|border="1" cellspacing="0" cellpadding="2"
|SAM/BAM/Uncompressed BAM from file
| <code>--in yourFileName</code>
|-
|SAM from stdin
| <code>--in -</code>
|-
|BAM from stdin
| <code>--in -.bam</code>
|-
|Uncompressed BAM from stdin
| <code>--in -.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.

← Older revision		Revision as of 22:30, 8 April 2019
Line 4:		Line 4:
	Use <code>{{{param\|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}		Use <code>{{{param\|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}

	The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|}}} .\|, unless your input file is stdin.}}		The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|}}} \|.\|, unless your input file is stdin.}}

	{{#if: {{{noStdin\|}}}\|This tool does not support input from stdin.\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}		{{#if: {{{noStdin\|}}}\|This tool does not support input from stdin.\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}

← Older revision		Revision as of 16:53, 6 January 2014
Line 1:		Line 1:
	{{{hdr\|===}}} Input File ({{#if: {{{noParam\|}}} \| {{{noParam}}} ~~Parameter~~\|<code>{{{param\|--in}}}</code>}}) {{{hdr\|===}}}		{{{hdr\|===}}} Input File ({{#if: {{{noParam\|}}} \| {{{noParam}}} argument\|<code>{{{param\|--in}}}</code>}}) {{{hdr\|===}}}

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

← Older revision		Revision as of 22:29, 8 April 2019
Line 4:		Line 4:
	Use <code>{{{param\|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}		Use <code>{{{param\|--in}}}</code> followed by your file name to specify the SAM/BAM input file.}}

	The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|.}}}\|, unless your input file is stdin.}}		The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user{{#if: {{{noStdin\|}}} .\|, unless your input file is stdin.}}

	{{#if: {{{noStdin\|This tool does not support input from stdin.~~}}}~~\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}		{{#if: {{{noStdin\|}}}\|This tool does not support input from stdin.\|A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).}}

	{\|border="1" cellspacing="0" cellpadding="2"		{\|border="1" cellspacing="0" cellpadding="2"
	\|SAM/BAM/Uncompressed BAM from file		\|SAM/BAM/Uncompressed BAM from file
	\| <code>{{#if: {{{noParam\|}}} \| \|--in}} yourFileName</code>		\| <code>{{#if: {{{noParam\|}}} \| \|--in}} yourFileName</code>
	\|-		{{#if: {{{noStdin\|}}} \| \|<tr>
	\|{{#if: {{{noStdin\|}}} \| \|SAM from stdin}}		<td>SAM from stdin</td>
	~~\|{{#if: {{{noStdin\|}}} \| \|~~<code>{{#if: {{{noParam\|}}} \| \|--in}} -</code>}}		<td><code>{{#if: {{{noParam\|}}} \| \|--in}} -</code></td></tr>
	\|-		<tr>
	\|BAM from stdin		<td>BAM from stdin</td>
	\| <code>{{#if: {{{noParam\|}}} \| \|--in}} -.bam</code>		<td><code>{{#if: {{{noParam\|}}} \| \|--in}} -.bam</code></td></tr>
	\|-		<tr>
	\|Uncompressed BAM from stdin		<td>Uncompressed BAM from stdin</td>
	\| <code>{{#if: {{{noParam\|}}} \| \|--in}} -.ubam</code>		<td><code>{{#if: {{{noParam\|}}} \| \|--in}} -.ubam</code></td></tr>}}
	\|}		\|}


	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.