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| = Usage = | | = Usage = |
| ./bam gapInfo --in <inputFile> --out <outputFile> [--noeof] [--params] | | ./bam gapInfo --in <inputFile> --out <outputFile> [--noeof] [--params] |
− |
| |
| | | |
| = Parameters = | | = Parameters = |
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| --out : the output file to be written | | --out : the output file to be written |
| Optional Parameters: | | Optional Parameters: |
− | --refFile : reference file, used to skip gaps that include reference base 'N' (for runs without --detailed) | + | --refFile : reference file, used to skip gaps that include reference base 'N' (for runs without --detailed) --detailed : Print the details for each read pair |
− | --detailed : Print the details for each read pair
| |
| Optional Parameters for the Detailed Option: | | Optional Parameters for the Detailed Option: |
| --checkFirst : Check the first in pair flag and print "NotFirst" if it isn't first | | --checkFirst : Check the first in pair flag and print "NotFirst" if it isn't first |
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| --noeof : Do not expect an EOF block on a bam file. | | --noeof : Do not expect an EOF block on a bam file. |
| --params : Print the parameter settings to stderr | | --params : Print the parameter settings to stderr |
− |
| |
| </pre> | | </pre> |
| + | {{PhoneHomeParamDesc}} |
| | | |
− | | + | == Required Parameters == |
| {{inBAMInputFile}} | | {{inBAMInputFile}} |
| | | |
− | == Output File (<code>--out</code>) == | + | === Output File (<code>--out</code>) === |
| Use <code>--out</code> followed by a file name to specify the output file to write. | | Use <code>--out</code> followed by a file name to specify the output file to write. |
| | | |
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| Detailed output does not have a header line and is described below under the [[#Print Detailed Per-Pair Information (<code>--detailed</code>) | --detailed]] parameter. | | Detailed output does not have a header line and is described below under the [[#Print Detailed Per-Pair Information (<code>--detailed</code>) | --detailed]] parameter. |
| | | |
| + | == Optional Prameters == |
| {{RefFile}} | | {{RefFile}} |
| | | |
| With this option specified, do not increment counters for the number of times that a gap is found if any of the reference bases in the gap are an 'N'. (N/A if <code>--detailed</code> is specified.) | | With this option specified, do not increment counters for the number of times that a gap is found if any of the reference bases in the gap are an 'N'. (N/A if <code>--detailed</code> is specified.) |
| | | |
− | == Print Detailed Per-Pair Information (<code>--detailed</code>) == | + | === Print Detailed Per-Pair Information (<code>--detailed</code>) === |
| With this option, for every record processed per the above rules, the following information is printed on a line as tab separated columns: | | With this option, for every record processed per the above rules, the following information is printed on a line as tab separated columns: |
| * Reference/Chromosome Name | | * Reference/Chromosome Name |
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| Detailed output does not have a header line. | | Detailed output does not have a header line. |
| | | |
− | == (<code>--checkFirst</code>) ==
| + | See [[#Optional Parameters for --detailed|Optional Parameters for <code>--detailed</code>]] for additional options related to <code>--detailed</code>. |
− | Only applicable if <code>--detailed</code> is also provided.
| |
| | | |
− | When specified along with <code>--detailed</code>, the output for each record processed also includes "NotFirst" if it is not marked as FirstFragment in the flags.
| + | {{noeofBGZFParameter}} |
| + | {{paramsParameter}} |
| | | |
− | == (<code>--checkStrand</code>) == | + | == Optional Parameters for [[#Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] == |
− | Only applicable if <code>--detailed</code> is also provided. | + | === Check First (<code>--checkFirst</code>) === |
| + | Only applicable if [[Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] is also provided. |
| | | |
− | When specified along with <code>--detailed</code>, the output for each record processed also includes "Reverse" if it is marked as the reverse strand in the flags. | + | When specified along with [Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]], the output for each record processed also includes "NotFirst" if it is not marked as FirstFragment in the flags. |
| | | |
− | {{noeofBGZFParameter}}
| + | === Check Strand (<code>--checkStrand</code>) === |
− | {{paramsParameter}} | + | Only applicable if [Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]] is also provided. |
| + | |
| + | When specified along with [Print Detailed Per-Pair Information (--detailed)|<code>--detailed</code>]], the output for each record processed also includes "Reverse" if it is marked as the reverse strand in the flags. |
| + | |
| + | {{PhoneHomeParameters}} |
| | | |
| = Return Value = | | = Return Value = |