Merge branch 'release/v3.0.1'

milaboratory · Oct 25, 2018 · f826d72 · f826d72
2 parents 8ed81e7 + 3485afa
commit f826d72
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diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,14 @@
 
+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)
 ========================
 

diff --git a/doc/ExportFieldsClone.rst b/doc/ExportFieldsClone.rst
@@ -1,13 +1,9 @@
-+--------------------------+--------------------------------------------------------------------------------+
-| 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             |
++--------------------------+----------------------------+
diff --git a/doc/ExportFieldsVDJCAlignments.rst b/doc/ExportFieldsVDJCAlignments.rst
@@ -5,10 +5,6 @@
 +----------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
 | ``-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)                                                                            |

diff --git a/doc/ExportFieldsVDJCObject.rst b/doc/ExportFieldsVDJCObject.rst
@@ -89,9 +89,9 @@
 +---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``-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                                                                                                                                                                                                                                                                                                                                                                                                                                              |
 +---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -117,6 +117,10 @@
 +---------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``-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                                                                                                                                                                                                                                                                                                                                                                                                                                                          |