BamUtil: dumpAsp - Revision history

Mktrost at 21:39, 3 January 2014

2014-01-03T21:39:46Z

← Older revision		Revision as of 17:39, 3 January 2014
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	</pre>		</pre>

	== Asp File Name <code>(--asp)</code>==		== Required Parameters ==
			=== Asp File Name <code>(--asp)</code>===

	Use <code>--asp</code> followed by the file name of the ASP file that you want to read.		Use <code>--asp</code> followed by the file name of the ASP file that you want to read.

Mktrost at 21:39, 3 January 2014

2014-01-03T21:39:25Z

← Older revision		Revision as of 17:39, 3 January 2014
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	This option accepts both gzipped files and uncompressed files.		This option accepts both gzipped files and uncompressed files.

	== Only print Data Records <code>(--dataOnly)</code>==		== Optional Parameters ==
			=== Only print Data Records <code>(--dataOnly)</code>===
	The <code>--dataOnly</code> option tells the tool to print only Reference Only and Detailed records. Any Empty and Position records are not printed.		The <code>--dataOnly</code> option tells the tool to print only Reference Only and Detailed records. Any Empty and Position records are not printed.

Mktrost: /* Asp File Name (--asp) */

2012-01-27T20:47:40Z

Asp File Name (--asp)

← Older revision		Revision as of 16:47, 27 January 2012
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	Use <code>--asp</code> followed by the file name of the ASP file that you want to read.		Use <code>--asp</code> followed by the file name of the ASP file that you want to read.

			This option accepts both gzipped files and uncompressed files.

	== Only print Data Records <code>(--dataOnly)</code>==		== Only print Data Records <code>(--dataOnly)</code>==

Mktrost at 20:21, 27 January 2012

2012-01-27T20:21:28Z

← Older revision		Revision as of 16:21, 27 January 2012
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	= Overview of the <code>dumpAsp</code> function of <code>bamUtil</code> =		= Overview of the <code>dumpAsp</code> function of <code>bamUtil</code> =
	The <code>dumpAsp</code> option on the [[bamUtil]] executable prints the contents of an ASP file in a readable format to stdout.		The <code>dumpAsp</code> option on the [[bamUtil]] executable prints the contents of an [[LibStatGen: ASP\|ASP]] file in a readable format to stdout.

	<span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>		<span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>

Mktrost at 20:20, 27 January 2012

2012-01-27T20:20:27Z

← Older revision		Revision as of 16:20, 27 January 2012
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	= Overview of the <code>dumpAsp</code> function of <code>bamUtil</code> =		= Overview of the <code>dumpAsp</code> function of <code>bamUtil</code> =
	The <code>dumpAsp</code> option on the [[bamUtil]] executable prints the contents of an ASP file in a readable format to stdout.		The <code>dumpAsp</code> option on the [[bamUtil]] executable prints the contents of an ASP file in a readable format to stdout.

			<span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>

Mktrost: /* Output */

2012-01-27T17:06:14Z

Output

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	<code>DETAILED</code> records have 6 additional fields:		<code>DETAILED</code> records have 6 additional fields:
	# numBases - the number of bases at this position		# numBases - the number of bases at this position
	# bases - the bases at this position. String of ACTGND characters that is numBases long. ('D' represents a deletion.)		# bases - the bases at this position. String of ACTGND characters that is numBases long. ('D' represents a deletion)
	# qualities - the qualities at this position. String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)		# qualities - the qualities at this position. String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)
	# cycles - the cycles for this position. There are numBases cycles, separated by a ':'.		# cycles - the cycles for this position. There are numBases cycles, separated by a ':'. (-1 represents the cycle of a deletion)
	# strands - the strands for this position. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.		# strands - the strands for this position. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
	# mqs - the mapping qualities for this position. There are numBases mapping qualities, separated by a ':'.		# mqs - the mapping qualities for this position. There are numBases mapping qualities, separated by a ':'.

Mktrost: Created page with 'dumpAsp Category:BAM Software Category:Software = Overview of the `dumpAsp` function of `bamUtil` = The `dumpAsp` o…'

2012-01-27T17:05:04Z

Created page with 'dumpAsp Category:BAM Software Category:Software = Overview of the <code>dumpAsp</code> function of <code>bamUtil</code> = The <code>dumpAsp</code> o…'

New page

[[Category:BamUtil|dumpAsp]]
[[Category:BAM Software]]
[[Category:Software]]

= Overview of the <code>dumpAsp</code> function of <code>bamUtil</code> =
The <code>dumpAsp</code> option on the [[bamUtil]] executable prints the contents of an ASP file in a readable format to stdout.

= Usage =
./bam dumpAsp --asp <aspFile> [--params]

= Parameters =
<pre>
Required Parameters:
--asp : the path/name of the asp file to display
Optional Parameters:
--dataOnly : Only print the data records.
--params : print the parameter settings
</pre>

== Asp File Name <code>(--asp)</code>==

Use <code>--asp</code> followed by the file name of the ASP file that you want to read.

== Only print Data Records <code>(--dataOnly)</code>==
The <code>--dataOnly</code> option tells the tool to print only Reference Only and Detailed records. Any Empty and Position records are not printed.

{{paramsParameter}}

= Return Value =
* 0: the file was processed successfully.
* non-0: the file was not processed successfully.

=Output=
Each ASP record is printed on one line with each field separated by a <code>tab</code>.

The 1st field in the row is the chromosomeID and 0-based position separated by a ':'.

The 2nd field is the record type, <code>POS</code>, <code>EMPTY</code>, <code>REF_ONLY</code>, or <code>DETAILED</code>.

<code>POS</code> and <code>EMPTY</code> records have no additional columns.

<code>REF_ONLY</code> records have 3 additional fields:
# numBases - the number of bases at this position
# GLH - the GLH for this position
# GLA - the GLA for this position

<code>DETAILED</code> records have 6 additional fields:
# numBases - the number of bases at this position
# bases - the bases at this position. String of ACTGND characters that is numBases long. ('D' represents a deletion.)
# qualities - the qualities at this position. String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)
# cycles - the cycles for this position. There are numBases cycles, separated by a ':'.
# strands - the strands for this position. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
# mqs - the mapping qualities for this position. There are numBases mapping qualities, separated by a ':'.

==Sample Output==
Here is an example of printing all records.
<pre>
0:74 POS
0:74 REF_ONLY 1 3 30
0:75 REF_ONLY 2 6 64
0:76 DETAILED 2 GT >> 2:1 01 44:34
0:77 DETAILED 2 TG >> 3:2 01 44:34
0:78 REF_ONLY 2 6 67
0:79 DETAILED 1 A > 4 1 34
0:1010 POS
0:1010 DETAILED 1 C 6 0 0 0
0:1011 DETAILED 1 C > 1 0 0
0:1012 DETAILED 1 G 6 2 0 0
0:1013 DETAILED 1 A + 3 0 0
0:1014 DETAILED 1 A 4 4 0 0
0:1015 DETAILED 1 D -1 0 0
0:1016 DETAILED 1 D -1 0 0
0:1750 POS
0:1750 DETAILED 1 A ; 3 0 0
0:1751 DETAILED 1 C > 4 0 0
0:1752 DETAILED 1 G > 5 0 0
0:1753 DETAILED 1 T > 6 0 0
0:1754 REF_ONLY 1 3 33
0:10272 POS
0:10272 REF_ONLY 1 3 25
0:10273 REF_ONLY 1 3 33
0:10274 DETAILED 2 CT 66 2:0 00 0:0
0:10275 DETAILED 2 CA +> 3:1 00 0:0
0:10276 REF_ONLY 2 6 49
0:10277 DETAILED 2 DC + -1:3 00 0:0
0:10278 DETAILED 2 DT 4 -1:4 00 0:0
0:10279 EMPTY
0:10280 EMPTY
0:10281 EMPTY
0:10282 EMPTY
0:10283 EMPTY
0:10284 EMPTY
0:10285 DETAILED 1 T 6 0 0 33
0:10286 REF_ONLY 1 3 33
0:10287 REF_ONLY 1 3 25
0:10288 REF_ONLY 1 0 0
0:10289 REF_ONLY 1 3 23
0:10290 DETAILED 1 D -1 0 33
0:10291 DETAILED 1 D -1 0 33
1:74 POS
1:74 DETAILED 1 A 0 0 0
1:75 DETAILED 1 C 1 0 0
1:76 DETAILED 1 G 2 0 0
1:77 DETAILED 1 T 3 0 0
1:78 REF_ONLY 1 0 0
1:1750 POS
1:1750 DETAILED 1 A ; 3 0 0
1:1751 DETAILED 1 C > 4 0 0
1:1752 DETAILED 1 G > 5 0 0
1:1753 DETAILED 1 T > 6 0 0
1:1754 REF_ONLY 1 3 33
2:74 POS
2:74 DETAILED 1 A ; 3 0 0
2:75 DETAILED 1 C > 4 0 0
2:76 DETAILED 1 G > 5 0 0
2:77 DETAILED 1 T > 6 0 0
2:78 REF_ONLY 1 3 33
</pre>

Here is an example of printing only data (REC_ONLY and DETAILED) records.
<pre>
0:74 REF_ONLY 1 3 30
0:75 REF_ONLY 2 6 64
0:76 DETAILED 2 GT >> 2:1 01 44:34
0:77 DETAILED 2 TG >> 3:2 01 44:34
0:78 REF_ONLY 2 6 67
0:79 DETAILED 1 A > 4 1 34
0:1010 DETAILED 1 C 6 0 0 0
0:1011 DETAILED 1 C > 1 0 0
0:1012 DETAILED 1 G 6 2 0 0
0:1013 DETAILED 1 A + 3 0 0
0:1014 DETAILED 1 A 4 4 0 0
0:1015 DETAILED 1 D -1 0 0
0:1016 DETAILED 1 D -1 0 0
0:1750 DETAILED 1 A ; 3 0 0
0:1751 DETAILED 1 C > 4 0 0
0:1752 DETAILED 1 G > 5 0 0
0:1753 DETAILED 1 T > 6 0 0
0:1754 REF_ONLY 1 3 33
0:10272 REF_ONLY 1 3 25
0:10273 REF_ONLY 1 3 33
0:10274 DETAILED 2 CT 66 2:0 00 0:0
0:10275 DETAILED 2 CA +> 3:1 00 0:0
0:10276 REF_ONLY 2 6 49
0:10277 DETAILED 2 DC + -1:3 00 0:0
0:10278 DETAILED 2 DT 4 -1:4 00 0:0
0:10285 DETAILED 1 T 6 0 0 33
0:10286 REF_ONLY 1 3 33
0:10287 REF_ONLY 1 3 25
0:10288 REF_ONLY 1 0 0
0:10289 REF_ONLY 1 3 23
0:10290 DETAILED 1 D -1 0 33
0:10291 DETAILED 1 D -1 0 33
1:74 DETAILED 1 A 0 0 0
1:75 DETAILED 1 C 1 0 0
1:76 DETAILED 1 G 2 0 0
1:77 DETAILED 1 T 3 0 0
1:78 REF_ONLY 1 0 0
1:1750 DETAILED 1 A ; 3 0 0
1:1751 DETAILED 1 C > 4 0 0
1:1752 DETAILED 1 G > 5 0 0
1:1753 DETAILED 1 T > 6 0 0
1:1754 REF_ONLY 1 3 33
2:74 DETAILED 1 A ; 3 0 0
2:75 DETAILED 1 C > 4 0 0
2:76 DETAILED 1 G > 5 0 0
2:77 DETAILED 1 T > 6 0 0
2:78 REF_ONLY 1 3 33
</pre>

BamUtil: dumpAsp - Revision history

Mktrost at 21:39, 3 January 2014

Mktrost at 21:39, 3 January 2014

Mktrost: /* Asp File Name (--asp) */

Mktrost at 20:21, 27 January 2012

Mktrost at 20:20, 27 January 2012

Mktrost: /* Output */

Mktrost: Created page with 'dumpAsp Category:BAM Software Category:Software = Overview of the dumpAsp function of bamUtil = The dumpAsp o…'

Mktrost: Created page with 'dumpAsp Category:BAM Software Category:Software = Overview of the `dumpAsp` function of `bamUtil` = The `dumpAsp` o…'