pipeline: new option "-report-all-metrics" added

CHANGES.txt

@@ -12,8 +12,10 @@
        - auN, auNG, auNA, auNGA (areas under the Nx/NGx/NAx/NGx curves; for more detail see
          https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity or the manual).
 
-      3. New option:
-       - "--local-mis-size" for setting minimal local misassembly size (default is 200, was 86).
+      3. New options:
+       - "--local-mis-size" for setting minimal local misassembly size (default is 200, was 86);
+       - "--report-all-metrics" for keeping the same content (list of metrics) in the main report
+         independently of inputs/options.
 
       4. MetaQUAST change:
        - preserving explicitly specified reference genomes in the reports (they were previously

manual.html

@@ -626,6 +626,15 @@ <h3>2.3 Command line options</h3>
     By default, the value is automatically detected as the median insert size of provided paired-end reads.
     If no paired-end reads are provided, 255 is used as the default value.
 
+<div class='option'>
+<code><b>--report-all-metrics</b></code>
+</div>
+Keep all quality metrics in the main report. Usually, all not-relevant metrics are not included in the report, e.g., reference-based metrics in the no-reference mode.
+Also, if metric values are undefined ('-') for all input assemblies, the metric is removed from the report.
+    The only exception from the latter rule is NG/NGA/LG/LGA-like metrics that explicitly contain '-' if reference was specified but (the aligned parts of) all assemblies are too small to reach, e.g., NG50 (NGA50).
+    <br>
+    The <code>--report-all-metrics</code> option changes this behaviour and forces QUAST (metaQUAST) to keep all metrics that can be reported in principle in the report. In this case, the number of rows in the main report is always the same independently of inputs and running mode/options, which simplifies automatic parsing of the report.
+
 <div class='option'>
 <code><b>--plots-format</b></code>  <code>&lt;format&gt;</code>
 </div>

quast_libs/options_parser.py

@@ -625,6 +625,10 @@ def parse_options(logger, quast_args):
              callback_kwargs={'min_value': qconfig.optimal_assembly_min_IS,
                               'max_value': qconfig.optimal_assembly_max_IS})
          ),
+        (['--report-all-metrics'], dict(
+            dest='report_all_metrics',
+            action='store_true')
+         ),
         (['--plots-format'], dict(
              dest='plot_extension',
              type='string',

quast_libs/qconfig.py

@@ -84,6 +84,7 @@
 run_busco = False
 large_genome = False
 use_kmc = False
+report_all_metrics = False
 
 # ideal assembly section
 optimal_assembly = False
@@ -486,6 +487,8 @@ def usage(show_hidden=False, mode=None, short=True, stream=sys.stdout):
         stream.write("    --upper-bound-min-con  <int>      Minimal number of 'connecting reads' needed for joining upper bound contigs into a scaffold\n")
         stream.write("                                      [default: %d for mate-pairs and %d for long reads]\n" % (MIN_CONNECT_MP, MIN_CONNECT_LR))
         stream.write("    --est-insert-size  <int>          Use provided insert size in upper bound assembly simulation [default: auto detect from reads or %d]\n" % optimal_assembly_default_IS)
+        stream.write("    --report-all-metrics              Keep all quality metrics in the main report even if their values are '-' for all assemblies or \n"
+                     "                                      if they are not applicable (e.g., reference-based metrics in the no-reference mode)\n")
         stream.write("    --plots-format  <str>             Save plots in specified format [default: %s].\n" % plot_extension)
         stream.write("                                      Supported formats: %s\n" % ', '.join(supported_plot_extensions))
         stream.write("    --memory-efficient                Run everything using one thread, separately per each assembly.\n")
@@ -506,7 +509,7 @@ def usage(show_hidden=False, mode=None, short=True, stream=sys.stdout):
         stream.write("    --sam     <filename,filename,...> Comma-separated list of SAM alignment files obtained by aligning reads to assemblies\n"
                          "                                      (use the same order as for files with contigs)\n")
         stream.write("    --bam     <filename,filename,...> Comma-separated list of BAM alignment files obtained by aligning reads to assemblies\n"
-                         "                                      (use the same order as for files with contigs)\n")
+                     "                                      (use the same order as for files with contigs)\n")
         stream.write("                                      Reads (or SAM/BAM file) are used for structural variation detection and\n")
         stream.write("                                      coverage histogram building in Icarus\n")
         stream.write("    --sv-bedpe  <filename>            File with structural variations (in BEDPE format)\n")

quast_libs/reporting.py

@@ -457,6 +457,10 @@ def table(order=Fields.order, ref_name=None):
     required_fields = []
 
     def define_required_fields():
+        if qconfig.report_all_metrics:
+            required_fields.extend(Fields.order)
+            return
+
         # if a reference is specified, keep the same number of Nx/Lx-like genome-based metrics in different reports
         # (no matter what percent of the genome was assembled)
         report = get(assembly_fpaths[0], ref_name=ref_name)