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Merge branch 'release/v3.0.1'
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dbolotin committed Oct 25, 2018
2 parents 8ed81e7 + 3485afa commit f826d72
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10 changes: 10 additions & 0 deletions CHANGELOG
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MiXCR 3.0.1 (25 Oct 2018)
========================

-- This fixes problem with repeated CLI options in export
-- `VRegionWithP` now is used as `featureToAlign` for V gene
-- `VTranscriptWithP` instead of `VTranscriptWithout5UTRWithP` used for RNA-Seq parameters
-- Rename `-sequence` to `-targetSequences` and `-quality` to `-targetQualities` in export #298
-- Minor cosmetics for clone ordering #401


MiXCR 3.0 (23 Oct 2018)
========================

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22 changes: 9 additions & 13 deletions doc/ExportFieldsClone.rst
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+--------------------------+--------------------------------------------------------------------------------+
| Field name | Description |
+==========================+================================================================================+
| ``-cloneId`` | Unique clone identifier |
+--------------------------+--------------------------------------------------------------------------------+
| ``-count`` | Clone count |
+--------------------------+--------------------------------------------------------------------------------+
| ``-fraction`` | Clone fraction |
+--------------------------+--------------------------------------------------------------------------------+
| ``-sequence`` | Aligned sequence (initial read), or 2 sequences in case of paired-end reads |
+--------------------------+--------------------------------------------------------------------------------+
| ``-quality`` | Initial read quality, or 2 qualities in case of paired-end reads |
+--------------------------+--------------------------------------------------------------------------------+
+--------------------------+----------------------------+
| Field name | Description |
+==========================+============================+
| ``-cloneId`` | Unique clone identifier |
+--------------------------+----------------------------+
| ``-count`` | Clone count |
+--------------------------+----------------------------+
| ``-fraction`` | Clone fraction |
+--------------------------+----------------------------+
4 changes: 0 additions & 4 deletions doc/ExportFieldsVDJCAlignments.rst
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+----------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| ``-readIds`` | Id(s) of read(s) corresponding to alignment |
+----------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| ``-sequence`` | Aligned sequence (initial read), or 2 sequences in case of paired-end reads |
+----------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| ``-quality`` | Initial read quality, or 2 qualities in case of paired-end reads |
+----------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| ``-descrR1`` | Description line from initial .fasta or .fastq file (deprecated) |
+----------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| ``-descrR2`` | Description line from initial .fasta or .fastq file (deprecated) |
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8 changes: 6 additions & 2 deletions doc/ExportFieldsVDJCObject.rst
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+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-aaFeature`` ``<gene_feature>`` | Amino acid sequence of specified gene feature |
+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-nFeatureImputed`` ``<gene_feature>`` | Nucleotide sequence of specified gene feature using letters from germline (marked lowercase) for unaligned regions |
| ``-nFeatureImputed`` ``<gene_feature>`` | Nucleotide sequence of specified gene feature using letters from germline (marked lowercase) for uncovered regions |
+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-aaFeatureImputed`` ``<gene_feature>`` | Amino acid sequence of specified gene feature using letters from germline (marked lowercase) for unaligned regions |
| ``-aaFeatureImputed`` ``<gene_feature>`` | Amino acid sequence of specified gene feature using letters from germline (marked lowercase) for uncovered regions |
+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-minFeatureQuality`` ``<gene_feature>`` | Minimal quality of specified gene feature |
+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-defaultAnchorPoints`` | Outputs a list of default reference points (like CDR2Begin, FR4End, etc. see documentation for the full list and formatting) |
+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-targetSequences`` | Aligned sequences (targets), separated with comma |
+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-targetQualities`` | Aligned sequence (target) qualities, separated with comma |
+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-vIdentityPercents`` | V alignment identity percents |
+---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-dIdentityPercents`` | D alignment identity percents |
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