BamUtil: dumpAsp
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:
- numBases - the number of bases at this position
- GLH - the GLH for this position
- GLA - the GLA for this position
DETAILED
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 ':'. (-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.
- 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