Line 7: |
Line 7: |
| | | |
| <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> |
| + | |
| + | |
| + | == Rules == |
| + | |
| + | '''Dealing with 'N' Bases''' |
| + | * If the reference is 'N': |
| + | ** Do Not write REF_ONLY or DETAILED records |
| + | ** Either write EMPTY or no record (depending on Gap Size and the next data record) |
| + | * If all reads at this position are 'N': |
| + | ** Either write EMPTY or no record (depending on Gap Size and the next data record) |
| + | * If some reads are 'N' and the rest are the reference (not 'N') |
| + | ** Write a REF_ONLY record but do not include the 'N's in the numBases |
| + | * If some reads are 'N' and some are non-reference (not 'N') |
| + | ** DEFAULT: Write a DETAILED record and include the 'N's in the numBases |
| + | ** OPTIONAL: Write a DETAILED record but do not include the 'N's in the numBases |
| | | |
| | | |
Line 32: |
Line 47: |
| </pre> | | </pre> |
| | | |
| + | == Required Parameters == |
| {{inBAMInputFile}} | | {{inBAMInputFile}} |
| | | |
− | == output File <code>(--out)</code>== | + | === output File <code>(--out)</code>=== |
| | | |
| Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup. | | Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup. |
Line 41: |
Line 57: |
| | | |
| {{RefFile}} | | {{RefFile}} |
| + | |
| + | == Optional Parameters == |
| {{BamIndex}} | | {{BamIndex}} |
| | | |
− | == Region List <code>(--regionList)</code> == | + | === Region List <code>(--regionList)</code> === |
| Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file. The region list file has one region on each line. | | Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file. The region list file has one region on each line. |
| | | |
Line 56: |
Line 74: |
| If a position is covered by multiple regions, the position will be piled up multiple times (once for each region). | | If a position is covered by multiple regions, the position will be piled up multiple times (once for each region). |
| | | |
− | == Gap Size <code>(--gapSize)</code> == | + | === Gap Size <code>(--gapSize)</code> === |
| When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them. | | When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them. |
| # Write an Empty record indicating no data for that position. | | # Write an Empty record indicating no data for that position. |
Line 74: |
Line 92: |
| | | |
| =Output= | | =Output= |
− | An [[LibStatGen: ASP|ASP]] file is written containing the pileup for the specified BAM file. | + | An [[LibStatGen: ASP|ASP]] file is written containing the pileup for the specified BAM file. ASP files are by default compressed using BGZF. |
| + | |
| + | The number of each type of record is output to stderr. |
| + | |
| + | For example: |
| + | <pre> |
| + | Number of Position Records = 6 |
| + | Number of Empty Records = 39 |
| + | Number of Reference Only Records = 12 |
| + | Number of Detailed Records = 29 |
| + | </pre> |