consistency, fetch_bed, build_tree

new consistency feature to write the variant count in the output tsv fixed fetch_bed error so that works altered build_region_tree logic so that bed chromosomes which aren't present in the baseline vcf's header are excluded more cleaning and documentation
ACEnglish · Jan 8, 2025 · 2932104 · 2932104
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diff --git a/docs/api/truvari.examples.rst b/docs/api/truvari.examples.rst
@@ -92,7 +92,7 @@ If your regions of interest are stored in an in-memory object instead of a BED f
         count += 1
     print(f"Total of {count} variants")
 
-To iterate over variants that are not within the regions, use `vcf.fetch_regions(tree, within=False)`. Both of these
+To iterate over variants that are not within the regions, use `vcf.fetch_regions(tree, inside=False)`. Both of these
 fetch methods use heuristics to choose the more efficient fetching strategy of either seeking through the VCF file or
 streaming the entire file.
 

diff --git a/docs/api/truvari.package.rst b/docs/api/truvari.package.rst
@@ -54,20 +54,24 @@ Extra Methods
 
 .. autofunction:: best_seqsim
 
+.. autofunction:: build_region_tree
+
 .. autofunction:: read_bed_tree
 
 .. autofunction:: check_vcf_index
 
 .. autofunction:: chunker
 
-.. autofunction:: compress_index_vcf
-
 .. autofunction:: cmd_exe
 
+.. autofunction:: compress_index_vcf
+
 .. autofunction:: coords_within
 
 .. autofunction:: count_entries
 
+.. autofunction:: extend_region_tree
+
 .. autofunction:: file_zipper
 
 .. autofunction:: help_unknown_cmd
@@ -82,6 +86,8 @@ Extra Methods
 
 .. autofunction:: make_temp_filename
 
+.. autofunction:: merge_region_tree_overlaps
+
 .. autofunction:: msa2vcf
 
 .. autofunction:: opt_gz_open