turning sizemax default back on

I forgot that some callers will make entire chromosome inversion calls, which breaks the chunking strategy
ACEnglish · Feb 18, 2025 · 28b7777 · 28b7777
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diff --git a/docs/Updates.md b/docs/Updates.md
@@ -1,6 +1,19 @@
-# Truvari 5.1.1
+# Truvari 5.2.1
 *in progress*
 
+* Fixed FP BNDs being dropped [details](https://github.com/ACEnglish/truvari/discussions/263). 
+
+# Truvari 5.2.0
+*February 16, 2025*
+
+* The default `--align` method for `phab` and `bench` switched to POA. See [discussion](https://github.com/ACEnglish/truvari/discussions/261) for details.
+* Fix bug in `--pick ac` where FN/FP variants were not being counted/output.
+* Fix `--dup-to-ins` Ticket [#258](https://github.com/ACEnglish/truvari/issues/258)
+* `ga4gh` now also writes a variant count summary json
+
+# Truvari 5.1.1
+*February 5, 2025*
+
 * `bench`
   *  new automatic hook into the refine step via `truvari bench --refine`
 * `refine`

diff --git a/docs/bench.md b/docs/bench.md
@@ -149,13 +149,18 @@ Refining bench output
 =====================
 As described in the [[refine wiki|refine]], a limitation of Truvari bench is 1-to-1 variant comparison. However, `truvari refine` can harmonize the variants to give them more consistent representations. A bed file named `candidate.refine.bed` is created by `truvari bench` and holds a set of regions which may benefit from refinement. To use it, simply run
 ```bash
-truvari bench -b base.vcf.gz -c comp.vcf.gz -o result/
-truvari refine --regions result/candidate.refine.bed \
-               --reference reference.fasta \
-               --recount --use-region-coords \
-               result/
+truvari bench -b base.vcf.gz -c comp.vcf.gz --reference reference.fasta  -o result/
+truvari refine result/
+```
+
+Refine has a few parameters detailed in the [[refine wiki|refine]]. But if you'd ike to run refinement automatically with defaults, you can simply use
+```bash
+truvari bench -b base.vcf.gz 
+     -c comp.vcf.gz 
+     --reference reference.fasta 
+     -o result/
+     --refine
 ```
-See [[refine wiki|refine]] for details.
 
 Comparing Sequences of Variants
 ===============================

diff --git a/truvari/collapse.py b/truvari/collapse.py
@@ -482,7 +482,7 @@ def parse_args(args):
     filteg.add_argument("-s", "--sizemin", type=truvari.restricted_int, default=50,
                         help="Minimum variant size to consider for comparison (%(default)s)")
     filteg.add_argument("-S", "--sizemax", type=truvari.restricted_int, default=50000,
-                        help="Maximum variant size to consider for comparison (%(default)s)")
+                        help="Maximum variant size to consider for comparison (-1 = off; %(default)s)")
     filteg.add_argument("--passonly", action="store_true", default=False,
                         help="Only consider calls with FILTER == PASS")
 

diff --git a/truvari/variant_params.py b/truvari/variant_params.py
@@ -85,7 +85,7 @@ class VariantParams():
         "bnddist": 100,
         "sizemin": 50,
         "sizefilt": 30,
-        "sizemax": -1,
+        "sizemax": 50000,
         "passonly": False,
         "no_ref": False,
         "pick": "single",