picard-tools(1) [debian man page]

picard-tools(1) 						   User Commands						   picard-tools(1)

NAME

       picard-tools - manipulate SAM and BAM files

SYNOPSIS

       picard-tools COMMAND [OPTION]...

DESCRIPTION

       SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.

       Picard Tools includes these utilities to manipulate SAM and BAM files:
	AddOrReplaceReadGroups
	BamIndexStats
	BamToBfq
	BuildBamIndex
	CalculateHsMetrics
	CleanSam
	CollectAlignmentSummaryMetrics
	CollectGcBiasMetrics
	CollectInsertSizeMetrics
	CollectMultipleMetrics
	CollectRnaSeqMetrics
	CompareSAMs
	CreateSequenceDictionary
	ExtractIlluminaBarcodes
	EstimateLibraryComplexity
	ExtractSequences
	FastqToSam
	FixMateInformation
	IlluminaBasecallsToSam
	MarkDuplicates
	MeanQualityByCycle
	MergeBamAlignment
	MergeSamFiles
	NormalizeFasta
	QualityScoreDistribution
	ReorderSam
	ReplaceSamHeader
	RevertSam
	SamFormatConverter
	SamToFastq
	SortSam
	ValidateSamFile
	ViewSam

REPORTING BUGS

       samtools-devel@lists.sourceforge.net

COPYRIGHT

       Copyright 2010 The Broad Institute

SEE ALSO

       http://picard.sourceforge.net/

picard-tools 1.27						     July 2010							   picard-tools(1)

docidx_lang_faq(n)						Documentation tools						docidx_lang_faq(n)

__________________________________________________________________________________________________________________________________________________

NAME

       docidx_lang_faq - docidx language faq

DESCRIPTION

OVERVIEW

   WHAT IS THIS DOCUMENT?
       This  document  is  currently mainly a placeholder, to be filled with commonly asked questions about the docidx markup language and compan-
       ions, and their answers.

       Please report any questions (and, if possible, answers) we should consider for this document in the category  doctools  of  the	Tcllib	SF
       Trackers [http://sourceforge.net/tracker/?group_id=12883].

EXAMPLES

   WHERE DO I FIND DOCIDX EXAMPLES?
       We  have  no direct examples of documents written using docidx markup. However the doctools processor dtplite does generate keyword indices
       when processing a set of documents written in doctools markup. The intermediate files use docidx markup and are not deleted when generation
       completes. These files can therefore serve as examples.

       dtplite is distributed as part of Tcllib, so to get it you need one of

       [1]    A  CVS  snapshot	of  Tcllib.  How  to  retrieve	such  a  snapshot  and the tools required for this are described at http://source-
	      forge.net/cvs/?group_id=12883

       [2]    A Tcllib release archive. They are available at http://sourceforge.net/project/showfiles.php?group_id=12883

BUGS, IDEAS, FEEDBACK
       This document, will undoubtedly contain bugs and other problems.  Please report any such in the category doctools of the Tcllib SF Trackers
       [http://sourceforge.net/tracker/?group_id=12883].  Please also report any ideas for enhancements you may have for either the package and/or
       the documentation.

SEE ALSO

       docidx_lang_cmdref, docidx_lang_intro, docidx_lang_syntax

KEYWORDS

       docidx commands, docidx language, docidx markup, docidx syntax, examples, faq, markup, semantic markup

CATEGORY

       Documentation tools

COPYRIGHT

       Copyright (c) 2007 Andreas Kupries <andreas_kupries@users.sourceforge.net>

doctools								1.0							docidx_lang_faq(n)