fix bug where ambiguous got lumped with other

doc/pangenome.md

@@ -443,7 +443,7 @@ This command uses the spot market by specifying `:1.35` after the node type to b
 
 ### HPRC Graph: Splitting by Chromosome
 
-There are too many reference contigs to make a graph for each because of all the unplaced contigs in GRCh38.  Ideally, we would drop them but it simplifies some downstream pipelines that use tools that expect them to be in BAM headers etc. to just include them in the graph.  To do this, we use the `--otherContig` option to lump them all into a single job, and `--refContigs` to spell out all the contigs we want to treat separately.
+There are too many reference contigs to make a graph for each because of all the unplaced contigs in GRCh38.  Ideally, we would drop them but it simplifies some downstream pipelines that use tools that expect them to be in BAM headers etc. to just include them in the graph.  To do this, we use the `--otherContig` option to lump them all into a single job, and `--refContigs` to spell out all the contigs we want to treat separately.  Note that the final output will be the same whether or not `--otherContig` is used. This option serves only to reduce the number of output files (and therefore alignment jobs). 
 
 Also, the `--minIdentity` option is used to ignore PAF lines with < 75% identity. Using this stringency is only possible because `--base` was used with `cactus-graphmap`.
 

src/cactus/refmap/cactus_graphmap_split.py

@@ -192,7 +192,8 @@ def graphmap_split_workflow(job, options, config, seqIDMap, gfa_id, gfa_path, pa
     gather_fas_job = split_fas_job.addFollowOnJobFn(gather_fas, seqIDMap, split_gfa_job.rv(0), split_fas_job.rv(0), split_fas_job.rv(1))
 
     # lump "other" contigs together into one file (to make fewer align jobs downstream)
-    bin_other_job = gather_fas_job.addFollowOnJobFn(bin_other_contigs, ref_contigs, other_contig, gather_fas_job.rv(0), disk=(gfa_size + paf_size) * 2)
+    bin_other_job = gather_fas_job.addFollowOnJobFn(bin_other_contigs, config, ref_contigs, other_contig, gather_fas_job.rv(0),
+                                                    disk=(gfa_size + paf_size) * 2)
 
     # return all the files, as well as the 2 split logs
     return (seqIDMap, bin_other_job.rv(), split_gfa_job.rv(1), gather_fas_job.rv(1))
@@ -451,7 +452,7 @@ def gather_fas(job, seq_id_map, output_id_map, contig_fa_map, contig_size_map):
 
     return output_id_map, contig_size_table_id
 
-def bin_other_contigs(job, ref_contigs, other_contig, output_id_map):
+def bin_other_contigs(job, config, ref_contigs, other_contig, output_id_map):
     """ take all the other (ie non ref) contigs (in practice, unplaced bits of grch38) and merge them
     all up into a single "other" contig.  this avoids a 1000 align jobs getting created downstream. 
     Note we've moved this to the ned here (it used to be done usinc -c -o in rgfa-split) so as to
@@ -461,12 +462,14 @@ def bin_other_contigs(job, ref_contigs, other_contig, output_id_map):
     if not ref_contigs or not other_contig or not output_id_map:
         return output_id_map
 
+    amb_name = getOptionalAttrib(findRequiredNode(config.xmlRoot, "graphmap_split"), "ambiguousName", default="_AMBIGUOUS_")
+    
     ref_contigs = set(ref_contigs)
     other_contigs = set()
     merged_output_path_map = {} # map[TYPE][EVENT] = local file path
 
     for ref_contig in output_id_map.keys():
-        if ref_contig not in ref_contigs:
+        if ref_contig not in ref_contigs and ref_contig != amb_name:
             other_contigs.add(ref_contig)
             for type_key in output_id_map[ref_contig].keys():
                 if type_key == 'fa':