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but uses a lot of memory since it stores all the read names.
but uses a lot of memory since it stores all the read names.
--rmTags : Remove the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
--rmTags : Remove the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
Quality Binning Parameters (optional):
Quality Binning Parameters (optional):
Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used)
Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used)
--binMid : Use the mid point of the quality bin range for the quality value of the bin.
--binMid : Use the mid point of the quality bin range for the quality value of the bin.
--binHigh : Use the high end of the quality bin range for the quality value of the bin.
--binHigh : Use the high end of the quality bin range for the quality value of the bin.
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== Required Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile}}
{{outBAMOutputFile}}
{{outBAMOutputFile}}
==Optional Parameters==
{{refFile}}
=== Keep OQ Tag (<code>--keepOQ</code>) ===
Use <code>--keepOQ</code> to keep the OQ tag rather than removing it. By default, the OQ tag is removed.
=== Keep Duplicates (<code>--keepDups</code>) ===
Use <code>--keepDups</code> to keep records that are marked as duplicate (in the flag). By default, records marked as duplicate are removed.
=== Replace Read Names with Unique Integers (<code>--sReadName</code>, <code>--readName</code>) ===
Use <code>--sReadName</code> or <code>--readName</code> to replace read names with unique integers and write the mapping to the specified file.
<code>--sReadName</code> requires the input file to have been presorted by readname, but no validation is done to ensure proper sorting. If it is not sorted, a readname will get mapped to multiple new values.
<code>--readName</code> does not require the input file to have been presorted by readname, but uses a lot of memory since it stores all the read names in memory.
=== Remove Tags (<code>--rmTags</code>) ===
Use <code>--rmTags</code> followed by a list of tags separated by ';' to remove the specified tags. The tags should be formatted as: <code>Tag:Type"</code>
{{noeofBGZFParameter}}
{{paramsParameter}}
==Optional Quality Binning Parameters==
Optionally, Quality scores can be binned to reduce the number of possible quality scores.
=== Quality Score Bins (<code>--binQualS</code>, <code>--binQualF</code>)===
Use <code>--binQualS</code> or <code>--binQualF</code> to bin qualities by phred score, into the specified ranges (only one of the two options can be specified).
The ranges are specified by comma separated minimum phred score for the bin, example: 1,17,20,30,40,50,70
The first bin always starts at 0, so does not need to be specified.
By default, the bin value is the low end of the range. Use [[#Quality Score Bin Value (--binMid, --binHigh)|<code>--binMid</code> or <code>--binHigh</code>]] to change the value for the bin.
Use <code>--binQualS</code> followed by the comma-separated bin minimum phred scores to specify the ranges on the command line.
Use <code>--binQualF</code> followed by the filename to specify the ranges in a file.
=== Quality Score Bin Value (<code>--binMid</code>, <code>--binHigh</code>)===
By default the lowest number in a bin is used as the bin's value.
Use <code>--binMid</code> to use the mid point of the quality bin range for the quality value of the bin.
Use <code>--binHigh</code> to use the highest number in the quality bin for the quality value of the bin.
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
Returns the SamStatus for the reads/writes.
Returns the SamStatus for the reads/writes (0 for success, non-0 for failure).
