BamUtil: dumpAsp

From Genome Analysis Wiki
Revision as of 17:39, 3 January 2014 by Mktrost (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigationJump to search


Overview of the dumpAsp function of bamUtil

The dumpAsp option on the bamUtil executable prints the contents of an ASP file in a readable format to stdout.

ASP is a new format that is currently in production, so this tool is not yet available for public release.


Usage

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


Parameters

	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

Required Parameters

Asp File Name (--asp)

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

This option accepts both gzipped files and uncompressed files.

Optional Parameters

Only print Data Records (--dataOnly)

The --dataOnly option tells the tool to print only Reference Only and Detailed records. Any Empty and Position records are not printed.

Print the Program Parameters (--params)

Use --params to print the parameters for your program to stderr.

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 tab.

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

The 2nd field is the record type, POS, EMPTY, REF_ONLY, or DETAILED.

POS and EMPTY records have no additional columns.

REF_ONLY records have 3 additional fields:

  1. numBases - the number of bases at this position
  2. GLH - the GLH for this position
  3. GLA - the GLA for this position

DETAILED records have 6 additional fields:

  1. numBases - the number of bases at this position
  2. bases - the bases at this position. String of ACTGND characters that is numBases long. ('D' represents a deletion)
  3. qualities - the qualities at this position. String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)
  4. cycles - the cycles for this position. There are numBases cycles, separated by a ':'. (-1 represents the cycle of a deletion)
  5. strands - the strands for this position. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
  6. 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. 

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

Here is an example of printing only data (REC_ONLY and DETAILED) records. 

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
Retrieved from "http://genome.sph.umich.edu/w/index.php?title=BamUtil:_dumpAsp&oldid=9218"