From e0f9ce61c8766430a3b3f8c642f44d382e329e12 Mon Sep 17 00:00:00 2001
From: Adam English <ACEnglish@gmail.com>
Date: Sun, 11 Aug 2024 13:42:53 -0400
Subject: [PATCH] update bed parsing

slightly faster IntervalTree.from_tuples than .addi
---
 README.md                                |   1 +
 repo_utils/answer_key/anno/anno_bpovl.jl | Bin 2393 -> 2410 bytes
 truvari/annotations/density.py           |   4 ++--
 truvari/region_vcf_iter.py               |   7 +++++--
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index bdbc7227..69deb8d4 100644
--- a/README.md
+++ b/README.md
@@ -52,6 +52,7 @@ Use Truvari's comparison engine to consolidate redundant variants in a merged mu
  - [segment](https://github.com/acenglish/truvari/wiki/segment) - Normalization of SVs into disjointed genomic regions
  - [stratify](https://github.com/acenglish/truvari/wiki/stratify) - Count variants per-region in vcf
  - [divide](https://github.com/ACEnglish/truvari/wiki/divide) - Divide a VCF into independent shards
+ - [ga4gh](https://github.com/ACEnglish/truvari/wiki/ga4gh) - Consolidate benchmarking result VCFs
 
 ## 🔎 More Information
 
diff --git a/repo_utils/answer_key/anno/anno_bpovl.jl b/repo_utils/answer_key/anno/anno_bpovl.jl
index 00328b57e8e4ffe188c3641446f8c64abf7baf43..11e3e0c8fad7ccad07fddeb64c92f702ab60c767 100644
GIT binary patch
delta 278
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z{T~6iCr@M*pRB<uFnI<LLuo;N22>z0S&&tnk;bI70Mt@OC_S|b%E(Zitj+GgXfZj5
sT~|adL$MR$j|QgXywco)O1=2W`HVS}B{-%qT1{Tdq0i_v`7TEd0KvIFk^lez

delta 260
zcmaDQbW@0>fn{p+MiwqcrVPo+VvO;V_p;|~e#FSa%qTVaIg2WfLPv(8w?JtU)Bpe6
zlNYjzPqttcn7jgrp|l`B0|YQaX@SX#tm2F`CZz?Sw!x^WRZv!j%4BPH2S)SBHSD^=
kvKb1U5a%~ACFhmq7F6mj-pkI&XgPTwhd!g@<aZo30HFUg6aWAK

diff --git a/truvari/annotations/density.py b/truvari/annotations/density.py
index bab723ed..83d7c7cb 100644
--- a/truvari/annotations/density.py
+++ b/truvari/annotations/density.py
@@ -61,8 +61,8 @@ def density_main(args):
     # setting new indexes after masking
     new_tree = defaultdict(IntervalTree)
     cnt = 0
-    for chrom in tree:
-        for intv in tree[chrom]:
+    for chrom, intvs in tree.items():
+        for intv in intvs:
             for i in range(intv.begin, intv.end, args.stepsize):
                 new_tree[chrom].addi(
                     i, min(intv.end, i + args.windowsize), data=cnt)
diff --git a/truvari/region_vcf_iter.py b/truvari/region_vcf_iter.py
index 4f4e4ba1..3a0d29c0 100644
--- a/truvari/region_vcf_iter.py
+++ b/truvari/region_vcf_iter.py
@@ -103,7 +103,7 @@ def build_anno_tree(filename, chrom_col=0, start_col=1, end_col=2, one_based=Fal
     """
     idx = 0
     correction = 1 if one_based else 0
-    tree = defaultdict(IntervalTree)
+    ttree = defaultdict(list)
     for line in truvari.opt_gz_open(filename):
         if line.startswith(comment):
             continue
@@ -115,8 +115,11 @@ def build_anno_tree(filename, chrom_col=0, start_col=1, end_col=2, one_based=Fal
             m_idx = idxfmt.format(idx)
         else:
             m_idx = idx
-        tree[chrom].addi(start, end + 1, data=m_idx)
+        ttree[chrom].append((start, end + 1, m_idx))
         idx += 1
+    tree = {}
+    for chrom in ttree:
+        tree[chrom] = IntervalTree.from_tuples(ttree[chrom])
     return tree, idx