Release 1.4.0

CHANGELOG.md

@@ -8,6 +8,9 @@ The meaning of each entry is user-based and can be found in our
 
 ## [Unreleased]
 
+
+## [1.4.0]
+
 ### Changed
 - Read filters does not support short arguments anymore (GATK update)
 
@@ -253,3 +256,4 @@ First pre-release
 [1.2.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.2.0
 [1.2.1]: https://github.com/magicDGS/ReadTools/releases/tag/1.2.1
 [1.3.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.3.0
+[1.4.0]: https://github.com/magicDGS/ReadTools/releases/tag/1.4.0

docs/_data/index.yml

@@ -1,128 +1,185 @@
 ReadTools:
-  version: 1.3.0
-  timestamp: 25-37-2018 02:37:45
+  version: 1.4.0
+  timestamp: 05-39-2018 02:39:16
 
 tools:
   - group: Diagnostics and Quality Control
-    summary: Tools that collect sequencing quality-related and comparative metrics
+    summary: Tools that collect sequencing quality related and comparative metrics
     components:
       - name: QualityEncodingDetector
         summary: Detects the quality encoding format for all kind of sources for ReadTools.
+        status: 'null'
   - group: Distmap integration
     summary: Tools for integration with the DistMap (Pandey & Schlötterer 2013).
     components:
       - name: DownloadDistmapResult
         summary: Download, sort and merge the alignments generated by DistMap.
+        status: 'null'
       - name: ReadsToDistmap
         summary: Converts any kind of ReadTools source to Distmap format.
+        status: 'null'
+  - group: Mapped reads
+    summary: Tools operating on already mapped reads (SAM/BAM/CRAM only)
+    components:
+      - name: ComputeProperStatByWindow
+        summary: Computes proper-paired reads statistics over windows 
+        status: '_**EXPERIMENTAL**_'
   - group: Reads conversion
     summary: Tools for converting any supported read source (SAM/BAM/CRAM/FASTQ)
     components:
       - name: ReadsToFastq
         summary: Converts any kind of ReadTools source to FASTQ format.
+        status: 'null'
       - name: StandardizeReads
         summary: Standardizes quality and format for all kind of sources for ReadTools.
+        status: 'null'
   - group: Reads manipulation
     summary: Tools for manipulating any supported read source (SAM/BAM/CRAM/FASTQ)
     components:
       - name: AssignReadGroupByBarcode
         summary: Assigns read groups based on barcode tag(s) for all kind of sources for ReadTools.
+        status: 'null'
       - name: TrimReads
         summary: Applies a trimming pipeline to any kind of sources for ReadTools
+        status: 'null'
 
 utilities:
   - group: Read Filters
     summary: Applied by engine to select reads for analysis
     components:
       - name: AlignmentAgreesWithHeaderReadFilter
         summary: Filters out reads where the alignment does not match the contents of the header
+        status: 'null'
       - name: AllowAllReadsReadFilter
         summary: Do not filter out any read
+        status: 'null'
       - name: AmbiguousBaseReadFilter
         summary: Filters out reads that have greater than the threshold number of N bases
+        status: 'null'
       - name: CigarContainsNoNOperator
         summary: Filter out reads with CIGAR containing N operator
+        status: 'null'
       - name: FirstOfPairReadFilter
         summary: Keep only reads that are first of pair
+        status: 'null'
       - name: FragmentLengthReadFilter
         summary: Keep only read pairs with insert length less than or equal to the given value
+        status: 'null'
       - name: GoodCigarReadFilter
         summary: Keep only reads containing good CIGAR string
+        status: 'null'
       - name: HasReadGroupReadFilter
         summary: Filter out reads without Read Group
+        status: 'null'
       - name: LibraryReadFilter
         summary: Keep only reads from the specified library
+        status: 'null'
       - name: MappedReadFilter
         summary: Filter out unmapped reads
+        status: 'null'
       - name: MappingQualityAvailableReadFilter
         summary: Filter out reads without available mapping quality
+        status: 'null'
       - name: MappingQualityNotZeroReadFilter
         summary: Filter out reads with mapping quality equal to zero
+        status: 'null'
       - name: MappingQualityReadFilter
         summary: Keep only reads with mapping qualities within a specified range
+        status: 'null'
       - name: MatchingBasesAndQualsReadFilter
         summary: Filter out reads where the bases and qualities do not match
+        status: 'null'
       - name: MateDifferentStrandReadFilter
         summary: Keep only reads with mates mapped on the different strand
+        status: 'null'
       - name: MateOnSameContigOrNoMappedMateReadFilter
         summary: Keep only reads whose mate maps to the same contig or is unmapped
+        status: 'null'
       - name: MetricsReadFilter
         summary: Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments
+        status: 'null'
       - name: NonZeroFragmentLengthReadFilter
         summary: Filter out reads with fragment length different from zero
+        status: 'null'
       - name: NonZeroReferenceLengthAlignmentReadFilter
         summary: Filter out reads that do not align to the reference
+        status: 'null'
       - name: NotDuplicateReadFilter
         summary: Filter out reads marked as duplicate
+        status: 'null'
       - name: NotSecondaryAlignmentReadFilter
         summary: Filter out reads representing secondary alignments
+        status: 'null'
       - name: NotSupplementaryAlignmentReadFilter
         summary: Filter out reads representing supplementary alignments
+        status: 'null'
       - name: OverclippedReadFilter
         summary: Filter out reads that are over-soft-clipped
+        status: 'null'
       - name: PairedReadFilter
         summary: Filter out unpaired reads
+        status: 'null'
       - name: PassesVendorQualityCheckReadFilter
         summary: Filter out reads failing platfor/vendor quality checks
+        status: 'null'
       - name: PlatformReadFilter
         summary: Keep only reads with matching Read Group platform
+        status: 'null'
       - name: PlatformUnitReadFilter
         summary: Filter out reads with matching platform unit attribute
+        status: 'null'
       - name: PrimaryLineReadFilter
         summary: Keep only reads representing primary alignments (those that satisfy both the NotSecondaryAlignment and  NotSupplementaryAlignment filters, or in terms of SAM flag values, must have neither of the 0x100 or  0x800 flags set).
+        status: 'null'
       - name: ProperlyPairedReadFilter
         summary: Keep only reads that are properly paired
+        status: 'null'
       - name: ReadGroupBlackListReadFilter
         summary: Keep records not matching the read group tag and exact match string.
+        status: 'null'
       - name: ReadGroupReadFilter
         summary: Keep only reads from the specified read group
+        status: 'null'
       - name: ReadLengthEqualsCigarLengthReadFilter
         summary: Filter out reads  where the read and CIGAR do not match in length
+        status: 'null'
       - name: ReadLengthReadFilter
         summary: Keep only reads whose length is within a certain range
+        status: 'null'
       - name: ReadNameReadFilter
         summary: Keep only reads with this read name
+        status: 'null'
       - name: ReadStrandFilter
         summary: Keep only reads whose strand is as specified
+        status: 'null'
       - name: SampleReadFilter
         summary: Keep only reads for a given sample
+        status: 'null'
       - name: SecondOfPairReadFilter
         summary: Keep only paired reads that are second of pair
+        status: 'null'
       - name: SeqIsStoredReadFilter
         summary: Keep only reads with sequenced bases
+        status: 'null'
       - name: ValidAlignmentEndReadFilter
         summary: Keep only reads where the read end is properly aligned
+        status: 'null'
       - name: ValidAlignmentStartReadFilter
         summary: Keep only reads with a valid alignment start
+        status: 'null'
       - name: WellformedReadFilter
         summary: Keep only reads that are well-formed
+        status: 'null'
   - group: Trimmers
     summary: Algorithms used to trim the reads.
     components:
       - name: CutReadTrimmer
         summary: Crops a concrete number of bases at the end of the read.
+        status: 'null'
       - name: MottQualityTrimmer
         summary: Trims low quality ends using the Mott's algorithm.
+        status: 'null'
       - name: TrailingNtrimmer
         summary: Trims the end of the read containing unknown bases.
+        status: 'null'
 

docs/javadoc/allclasses-frame.html

@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_60) on Wed Apr 25 14:37:40 CEST 2018 -->
-<title>All Classes (ReadTools 1.3.0 API)</title>
-<meta name="date" content="2018-04-25">
+<!-- Generated by javadoc (1.8.0_60) on Tue Jun 05 14:39:13 CEST 2018 -->
+<title>All Classes (ReadTools 1.4.0 API)</title>
+<meta name="date" content="2018-06-05">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -21,8 +21,12 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="org/magicdgs/readtools/tools/barcodes/dictionary/BarcodeDictionaryFactory.html" title="class in org.magicdgs.readtools.tools.barcodes.dictionary" target="classFrame">BarcodeDictionaryFactory</a></li>
 <li><a href="org/magicdgs/readtools/tools/barcodes/dictionary/decoder/BarcodeMatch.html" title="class in org.magicdgs.readtools.tools.barcodes.dictionary.decoder" target="classFrame">BarcodeMatch</a></li>
 <li><a href="org/magicdgs/readtools/metrics/barcodes/BarcodeStat.html" title="class in org.magicdgs.readtools.metrics.barcodes" target="classFrame">BarcodeStat</a></li>
+<li><a href="org/magicdgs/readtools/utils/function/BinaryPredicate.html" title="interface in org.magicdgs.readtools.utils.function" target="classFrame"><span class="interfaceName">BinaryPredicate</span></a></li>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/CheckQualityReadTransformer.html" title="class in org.magicdgs.readtools.utils.read.transformer" target="classFrame">CheckQualityReadTransformer</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/filter/CompletelyTrimReadFilter.html" title="class in org.magicdgs.readtools.utils.read.filter" target="classFrame">CompletelyTrimReadFilter</a></li>
+<li><a href="org/magicdgs/readtools/tools/mapped/ComputeProperStatByWindow.html" title="class in org.magicdgs.readtools.tools.mapped" target="classFrame">ComputeProperStatByWindow</a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/singlestat/ContainIndelCounter.html" title="class in org.magicdgs.readtools.utils.read.stats.singlestat" target="classFrame">ContainIndelCounter</a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/singlestat/ContainSoftclipCounter.html" title="class in org.magicdgs.readtools.utils.read.stats.singlestat" target="classFrame">ContainSoftclipCounter</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/CutReadTrimmer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming" target="classFrame">CutReadTrimmer</a></li>
 <li><a href="org/magicdgs/readtools/utils/distmap/DistmapEncoder.html" title="class in org.magicdgs.readtools.utils.distmap" target="classFrame">DistmapEncoder</a></li>
 <li><a href="org/magicdgs/readtools/utils/distmap/DistmapException.html" title="class in org.magicdgs.readtools.utils.distmap" target="classFrame">DistmapException</a></li>
@@ -43,10 +47,15 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="org/magicdgs/readtools/utils/HadoopUtils.html" title="class in org.magicdgs.readtools.utils" target="classFrame">HadoopUtils</a></li>
 <li><a href="org/magicdgs/readtools/utils/iterators/InterleaveGATKReadIterators.html" title="class in org.magicdgs.readtools.utils.iterators" target="classFrame">InterleaveGATKReadIterators</a></li>
 <li><a href="org/magicdgs/readtools/Main.html" title="class in org.magicdgs.readtools" target="classFrame">Main</a></li>
+<li><a href="org/magicdgs/readtools/cmd/programgroups/MappedProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups" target="classFrame">MappedProgramGroup</a></li>
 <li><a href="org/magicdgs/readtools/metrics/barcodes/MatcherStat.html" title="class in org.magicdgs.readtools.metrics.barcodes" target="classFrame">MatcherStat</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/MottQualityTrimmer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming" target="classFrame">MottQualityTrimmer</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/writer/NullGATKWriter.html" title="class in org.magicdgs.readtools.utils.read.writer" target="classFrame">NullGATKWriter</a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/PairEndReadStatFunction.html" title="interface in org.magicdgs.readtools.utils.read.stats" target="classFrame"><span class="interfaceName">PairEndReadStatFunction</span></a></li>
 <li><a href="org/magicdgs/readtools/utils/read/writer/PairEndSplitter.html" title="class in org.magicdgs.readtools.utils.read.writer" target="classFrame">PairEndSplitter</a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/pairstat/PairIntegerTagCounter.html" title="class in org.magicdgs.readtools.utils.read.stats.pairstat" target="classFrame">PairIntegerTagCounter</a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/pairstat/PairIntegerTagListCounter.html" title="class in org.magicdgs.readtools.utils.read.stats.pairstat" target="classFrame">PairIntegerTagListCounter</a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/engine/ProperStatWindowEngine.html" title="class in org.magicdgs.readtools.utils.read.stats.engine" target="classFrame">ProperStatWindowEngine</a></li>
 <li><a href="org/magicdgs/readtools/tools/quality/QualityEncodingDetector.html" title="class in org.magicdgs.readtools.tools.quality" target="classFrame">QualityEncodingDetector</a></li>
 <li><a href="org/magicdgs/readtools/cmd/argumentcollections/ReadGroupArgumentCollection.html" title="class in org.magicdgs.readtools.cmd.argumentcollections" target="classFrame">ReadGroupArgumentCollection</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/ReadReaderFactory.html" title="class in org.magicdgs.readtools.utils.read" target="classFrame">ReadReaderFactory</a></li>
@@ -61,6 +70,7 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="org/magicdgs/readtools/utils/iterators/ReadTransformerIterator.html" title="class in org.magicdgs.readtools.utils.iterators" target="classFrame">ReadTransformerIterator</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/ReadWriterFactory.html" title="class in org.magicdgs.readtools.utils.read" target="classFrame">ReadWriterFactory</a></li>
 <li><a href="org/magicdgs/readtools/utils/iterators/RecordToReadIterator.html" title="class in org.magicdgs.readtools.utils.iterators" target="classFrame">RecordToReadIterator</a></li>
+<li><a href="org/magicdgs/readtools/utils/math/RelationalOperator.html" title="enum in org.magicdgs.readtools.utils.math" target="classFrame">RelationalOperator</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/ReservedTags.html" title="class in org.magicdgs.readtools.utils.read" target="classFrame">ReservedTags</a></li>
 <li><a href="org/magicdgs/readtools/cmd/programgroups/RTConversionProgramGroup.html" title="class in org.magicdgs.readtools.cmd.programgroups" target="classFrame">RTConversionProgramGroup</a></li>
 <li><a href="org/magicdgs/readtools/engine/RTDataSource.html" title="class in org.magicdgs.readtools.engine" target="classFrame">RTDataSource</a></li>
@@ -77,14 +87,18 @@ <h1 class="bar">All&nbsp;Classes</h1>
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 <li><a href="org/magicdgs/readtools/cmd/argumentcollections/RTOutputFastqArgumentCollection.html" title="class in org.magicdgs.readtools.cmd.argumentcollections" target="classFrame">RTOutputFastqArgumentCollection</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read" target="classFrame">RTReadUtils</a></li>
+<li><a href="org/magicdgs/readtools/engine/RTReadWalker.html" title="class in org.magicdgs.readtools.engine" target="classFrame">RTReadWalker</a></li>
 <li><a href="org/magicdgs/readtools/cmd/RTStandardArguments.html" title="class in org.magicdgs.readtools.cmd" target="classFrame">RTStandardArguments</a></li>
 <li><a href="org/magicdgs/readtools/exceptions/RTUserExceptions.html" title="class in org.magicdgs.readtools.exceptions" target="classFrame">RTUserExceptions</a></li>
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 <li><a href="org/magicdgs/readtools/exceptions/RTUserExceptions.OutputFileExists.html" title="class in org.magicdgs.readtools.exceptions" target="classFrame">RTUserExceptions.OutputFileExists</a></li>
 <li><a href="org/magicdgs/readtools/engine/sourcehandler/SamSourceHandler.html" title="class in org.magicdgs.readtools.engine.sourcehandler" target="classFrame">SamSourceHandler</a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/SingleReadStatFunction.html" title="interface in org.magicdgs.readtools.utils.read.stats" target="classFrame"><span class="interfaceName">SingleReadStatFunction</span></a></li>
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 <li><a href="org/magicdgs/readtools/tools/conversion/StandardizeReads.html" title="class in org.magicdgs.readtools.tools.conversion" target="classFrame">StandardizeReads</a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/StatFunction.html" title="interface in org.magicdgs.readtools.utils.read.stats" target="classFrame"><span class="interfaceName">StatFunction</span></a></li>
+<li><a href="org/magicdgs/readtools/utils/read/stats/StatFunctionUtils.html" title="class in org.magicdgs.readtools.utils.read.stats" target="classFrame">StatFunctionUtils</a></li>
 <li><a href="org/magicdgs/readtools/utils/read/transformer/trimming/TrailingNtrimmer.html" title="class in org.magicdgs.readtools.utils.read.transformer.trimming" target="classFrame">TrailingNtrimmer</a></li>
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