Merge branch 'feature-a/2732-cli' into 'dev'

vidjil.cpp: refactor option handling using CLI11

Closes #2732, #2749, #2741, and #2738

See merge request !105

algo/core/dynprog.cpp

@@ -112,6 +112,15 @@ ostream& operator<<(ostream& out, const Cost& cost)
   return out;
 }
 
+string string_of_cost(const Cost cost)
+{
+   stringstream ss;
+   ss << cost ;
+   return ss.str();
+}
+
+
+
 Cost::Cost()
 {
 }

algo/core/dynprog.h

@@ -67,6 +67,7 @@ class Cost
 
 
 ostream& operator<<(ostream& out, const Cost& cost);
+string string_of_cost(const Cost cost);
 
 // Usual costs
 const Cost Hamming = Cost(0, -1, MINUS_INF);

algo/core/tools.h

@@ -8,6 +8,7 @@
 
 
 #define NO_LIMIT_VALUE  -1  // Value for 'all' on command-line options
+#define NO_LIMIT_VALUE_STRING  "-1"
 
 
 #define MAX_SEED_SIZE  50 // Spaced seed buffer

algo/tests/repseq_vdj.py

@@ -249,8 +249,8 @@ def header_igblast_results(ff_fasta, ff_igblast):
 
 ### Vidjil
 
-VIDJIL_FINE = '{directory}/vidjil-algo -X 100 -# "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
-VIDJIL_KMER = '{directory}/vidjil-algo -w 20 -# "#" -b out -c windows -uuuU -2 -g {directory}/germline/homo-sapiens.g %s > /dev/null ; cat out/out.segmented.vdj.fa out/out.unsegmented.vdj.fa >> %s'
+VIDJIL_FINE = '{directory}/vidjil-algo -X 100 --header-sep "#" -c segment -3 -d -g {directory}/germline/homo-sapiens.g %s >> %s'
+VIDJIL_KMER = '{directory}/vidjil-algo -w 20 --header-sep "#" -b out -c windows -uuuU -2 -g {directory}/germline/homo-sapiens.g %s > /dev/null ; cat out/out.segmented.vdj.fa out/out.unsegmented.vdj.fa >> %s'
 
 def should_results_from_vidjil_output(f_log):
     '''

algo/tests/should-get-tests/doc-examples.should-get

@@ -4,7 +4,7 @@
 # Test examples embedded in 'doc/algo.org'
 
 # Run eight times
-8:vidjil-algo -- V.D.J recombinations analysis
+8:vidjil-algo -- V.D.J recombinations analysis .*vidjil.org
 
 # '-c clone' (or implied), five times
 5: end of clones

algo/tests/should-get-tests/stanford-debug.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -\# FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa   $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --header-sep FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa   $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
 # Testing uncommon and debug options 
 
 $ verbose (-v)

algo/tests/should-get-tests/vidjil-custom-cost.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -f '1, 2, 3, 4, 5'
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -f '1, 2, 3, 4, 5' $VIDJIL_DATA/Stanford_S22.fasta
 !EXIT_CODE: 1
 
 $Check that correct custom cost is used

algo/tests/should-get-tests/vidjil-error-incorrect-germlines.should-get

-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/Makefile 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/Makefile $VIDJIL_DATA/Stanford_S22.fasta 2>&1
 !EXIT_CODE: 1
 
 $ Error, incorrect *.g

algo/tests/should-get-tests/vidjil-error-no-germline.should-get

 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS 2>&1
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS $VIDJIL_DATA/Stanford_S22.fasta 2>&1
 !EXIT_CODE: 1
 
 $ Error, no germlines

algo/tests/should-get-tests/vidjil-h-examples.should-get

 !NO_LAUNCHER:
-!LAUNCH: (cd $VIDJIL_DIR ; ./$EXEC -h 2>&1 > /dev/null | grep '$EXEC -c' | sed 's/X 50/X 5/' | sed 's/demo.LIL-L4/-X 1000 demo\/LIL-L4/' | sh)
+
+cd $VIDJIL_DIR
+./$EXEC -h | grep '$EXEC -c' | sed 's/X 50/X 5/' | sed 's/demo.LIL-L4/-X 1000 demo\/LIL-L4/' | sh
 
 # Test examples embedded in './vidjil-algo -h'
 

algo/tests/should-get-tests/vidjil-help-advanced.should-get

 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -H  2> out-v ; cat out-v
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -H
 
 $ License
 1:vidjil-algo is free software
@@ -8,4 +8,9 @@ $ Check default costs
 1:segmenter .* "4, -6, -10, -1, -10"
 1:clustering .* "1, -4, -4, 0, 0"
 
+$ Display advanced options
+: , experimental options
+: custom Cost
 
+$ Correct number of options
+B47:^  -

algo/tests/should-get-tests/vidjil-help.should-get

 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -h  2> out-v ; cat out-v
+!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -h
 
 $ License
 1:vidjil-algo is free software
 
 $ Check default filtering options
-1:minimal number of reads supporting a clone .*: 5
-1:minimal percentage of reads supporting a clone .*: 0
-1:maximal number of clones computed with a consensus sequence .*: 100
-1:maximal number of clones to be analyzed .*: 100
+1: =5 .* minimal number of reads supporting a clone
+1: =0 .* minimal percentage of reads supporting a clone
+1: =100 .* maximal number of clones computed with a consensus sequence
+1: =100 .* maximal number of clones to be analyzed
 
+$ Do not display advanced options
+0: , experimental options
+0: custom Cost
+
+$ Correct number of regular options
+B24:^  -

algo/tests/should-get-tests/vidjil_revcomp_s22.should-get

-!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log && $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' |  sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log && diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --ratio 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --ratio 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' |  sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log
+!LAUNCH: diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
 !EXIT_CODE: 1
 
 $ Same number segmented