Changes

* dropping OQ fields (default, disable using <code>--keepOQ</code>)

* dropping OQ fields (default, disable using <code>--keepOQ</code>)

* dropping duplicates (default, disable using <code>--keepDups</code>)

* dropping duplicates (default, disable using <code>--keepDups</code>)

* dropping specified tags (<code>--rmTags Tag1:Type1;Tag2:Type2</code>)

* dropping specified tags (<code>--rmTags "Tag1:Type1;Tag2:Type2"</code>)

* using '=' when a base matches the reference (<code>--refFile refFileName.fa</code>)

* using '=' when a base matches the reference (<code>--refFile refFileName.fa</code>)

* binning quality scores (<code>--binQualS</code><code>--binQualF</code>)

* binning quality scores (<code>--binQualS</code><code>--binQualF</code>)

= Usage =

= Usage =

  ./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <Tag:Type[;Tag:Type]*>] [--noeof] [--params]

  ./bam squeeze --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <refFilePath/Name>] [--keepOQ] [--keepDups] [--readName <readNameMapFile.txt>] [--sReadName <readNameMapFile.txt>] [--binQualS <minQualBin2>,<minQualBin3><...>] [--binQualF <filename>] [--rmTags <"Tag:Type[;Tag:Type]*>"] [--noeof] [--params]

                   This version does not require the input file to have been presorted by readname,

                   This version 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.

                   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.

--noeof      : do not expect an EOF block on a bam file.

--params    : print the parameter settings

--params    : print the parameter settings

--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.

</pre>

</pre>

== Required Parameters ==

== Required Parameters ==

=== Remove Tags (<code>--rmTags</code>) ===

=== 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>

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>.  Note: when using the ';' to specify multiple tags, be sure to put the whole string in quotes - otherwise the ';' will be interpreted as the end of the command.  Example: <code>--rmTags "OQ:Z;MD:Z"</code> or <code>--rmTags 'OQ:Z;MD:Z'</code>

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