Merge branch 'feature-a/3569-airr-unproductivity-causes' into 'dev'

More AIRR fields, unproductivity causes

Closes #3569

See merge request !879

algo/core/output.cpp

 #include "output.h"
+#include "segment.h"
 
 #define NULL_VAL ""
+#define AIRR_TRUE "T"
+#define AIRR_FALSE "F"
 
 string getout(json v)
 {
@@ -149,8 +152,8 @@ void SampleOutputVidjil::out(ostream &s, bool with_clones)
 
 string TF_format_bool(string val)
 {
-  if (val == "false") return "F" ;
-  if (val == "true") return "T" ;
+  if (val == "false") return AIRR_FALSE ;
+  if (val == "true") return AIRR_TRUE ;
   return val ;
 }
 
@@ -182,7 +185,18 @@ map <string, string> CloneOutputAIRR::fields()
   fields["cdr3_aa"] = get(KEY_SEG, "cdr3", "aa");
   fields["junction"] = NULL_VAL;
   fields["junction_aa"] = get(KEY_SEG, "junction", "aa");
+
   fields["productive"] = TF_format_bool(get(KEY_SEG, "junction", "productive"));
+  bool productive = (fields["productive"] == AIRR_TRUE); // thsus false for both AIRR_FALSE and NULL_VAL
+  string unproductive = get(KEY_SEG, "junction", "unproductive");
+  fields["vj_in_frame"] = productive ? AIRR_TRUE
+                        : unproductive == UNPROD_STOP_CODON ? AIRR_TRUE
+                        : unproductive == UNPROD_OUT_OF_FRAME ? AIRR_FALSE
+                        : NULL_VAL;
+  fields["stop_codon"] = productive ? AIRR_FALSE
+                       : unproductive == UNPROD_STOP_CODON ? AIRR_TRUE
+                       : NULL_VAL;
+
   fields["rev_comp"] = NULL_VAL;
 
   fields["warnings"] = getWarnings();
@@ -200,6 +214,7 @@ void SampleOutputAIRR::out(ostream &s)
     "sequence",
     
     "productive",
+    "vj_in_frame", "stop_codon",
     "junction_aa",
     "junction",
     "cdr3_aa",

algo/tests/should-get-tests/airr-S22.should

@@ -29,9 +29,9 @@ $ One clone has 8 reads, two clones have 5 reads
 1:IGH 8
 2:IGH 5
 
-$ Two clones are productive, no clone is labeled as non-productive
-2:\tT\t
-0:\tF\t
+$ Two clones are productive (productive, vj_in_frame, NOT stop_codon), no clone is labeled as non-productive
+2:\tT\tT\tF\t
+0:\tF\t[FT]\t[FT]\t
 
 $ v_call for 2 clones (-z 2)
 2:IGHV

algo/tests/should-get-tests/productive.should

@@ -17,4 +17,17 @@ $ Cause of unproductivity
 :clones[0].seg.junction.unproductive: stop-codon
 0:clones[1].seg.junction.unproductive
 :clones[2].seg.junction.unproductive: out-of-frame
-:clones[3].seg.junction.unproductive: too-short
\ No newline at end of file
+:clones[3].seg.junction.unproductive: too-short
+
+!OUTPUT_FILE: out/productive_stop_outframe.tsv
+!LAUNCH: echo
+!OPTIONS: --mod Jr
+
+$ Clone 001, AIRR: NOT productive, vdj_in_frame, stop_codon
+1:001.*\tF\tT\tT\t
+
+$ Clone 002, AIRR: productive, vdj_in_frame, NOT stop_codon
+1:002.*\tT\tT\tF\t
+
+$ Clone 003, AIRR: NOT productive, NOT vdj_in_frame, NULL stop_codon
+1:003.*\tF\tF\t\t

doc/vidjil-algo.md

@@ -724,6 +724,8 @@ Using `-c designations` trigger a separate analysis for each read, but this is u
 | cdr3_aa | string | Amino acid translation of the cdr3 field.   <br />*implemented*
 | cdr3_sequence_start, cdr3_sequence_end  | number |   Start/end position of the CDR3 in the query sequence (1-based closed interval).   <br />*implemented* |
 | productive | boolean | True if the V(D)J sequence is predicted to be productive.  <br /> *true, false, or null when no CDR3 has been detected* |
+| vj_in_frame | boolean | True if the V and J gene alignments are in-frame. <br /> *true, false, or null when no CDR3 has been detected* |
+| stop_codon | boolean | True if the aligned sequence contains a stop codon. <br /> *true, false, or null when vj_in_frame is false* |
 | sequence_alignment  | string  | Aligned portion of query sequence, including any indel corrections or numbering spacers, such as IMGT-gaps. Typically, this will include only the V(D)J region, but that is not a requirement. <br /> *null*                                         |
 | germline_alignment | string  | Assembled, aligned, fully length inferred germline sequence spanning the same region as the sequence_alignment field (typically the V(D)J region) and including the same set of corrections and spacers (if any). <br />*null*
 | v_cigar, d_cigar, j_cigar | string  | CIGAR strings for the V/D/J gene <br />*null*.