Update README in anticipation of Bioconda

Author: clintval

README.md

@@ -1,5 +1,7 @@
 # vartovcf
 
+[![Install with bioconda](https://img.shields.io/badge/Install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/recipes/vartovcf/README.html)
+[![Anaconda Version](https://anaconda.org/bioconda/vartovcf/badges/version.svg)](http://bioconda.github.io/recipes/vartovcf/README.html)
 [![Build Status](https://github.com/clintval/vartovcf/actions/workflows/rust.yml/badge.svg?branch=main)](https://github.com/clintval/vartovcf/actions/workflows/rust.yml)
 [![Coverage Status](https://coveralls.io/repos/github/clintval/vartovcf/badge.svg?branch=main)](https://coveralls.io/github/clintval/vartovcf?branch=main)
 [![Language](https://img.shields.io/badge/language-rust-a72144.svg)](https://www.rust-lang.org/)
@@ -9,14 +11,14 @@ Convert variants from VarDict/VarDictJava into VCF v4.2 format.
 ![The Pacific Northwest - Fish Lake](.github/img/cover.jpg)
 
 ```bash
-❯ VarDictJava/build/install/VarDict/bin/VarDict \
+❯ vardict-java \
     -b input.bam \
-    -G /references/hg38.fa \
+    -G hg38.fa \
     -N dna00001 \
     -c1 -S2 -E3 -g4 -f0.05 \
     --fisher \
     calling-intervals.bed \
-  | vartovcf -r /references/hg38.fa -s dna00001 \
+  | vartovcf --reference hg38.fa --sample dna00001 \
   | bcftools sort -Oz > variants.vcf.gz
 ```
 
@@ -31,20 +33,24 @@ Convert variants from VarDict/VarDictJava into VCF v4.2 format.
 #### Benchmarks
 
 ```bash
-❯ vartovcf -r /references/hs38DH.fa -s dna00001 < test.var > /dev/null
-[2021-01-31T03:45:12Z INFO  vartovcf] Input stream: STDIN
-[2021-01-31T03:45:12Z INFO  vartovcf] Output stream: STDOUT
-[2021-01-31T03:45:12Z INFO  vartovcflib::progress_logger] Logging records started at: 2021-01-30 22:45:12.
-[2021-01-31T03:45:17Z INFO  vartovcflib::progress_logger] Processed 100000 variant records. Elapsed time: 00:00:05. Time of last 100000 variant records: 00:00:05
-[2021-01-31T03:45:21Z INFO  vartovcflib::progress_logger] Processed 156471 variant records. Elapsed time: 00:00:08. Time of last 56471 variant records: 00:00:03
-
-❯ hyperfine --warmup 5 'vartovcf -r /references/hs38DH.fa -s dna00001 < test.var > /dev/null'
+❯ vartovcf --reference hs38DH.fa --sample dna00001 < test.var > /dev/null
+[2025-10-21T01:16:49Z INFO  vartovcf] Input stream: STDIN
+[2025-10-21T01:16:49Z INFO  vartovcf] Output stream: STDOUT
+[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 10000 variant records
+[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 20000 variant records
+[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 30000 variant records
+[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 40000 variant records
+[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 50000 variant records
+[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 60000 variant records
+[2025-10-21T01:16:49Z INFO  proglog] [main] Processed 60181 variant records
+
+❯ hyperfine --warmup 5 'vartovcf -r hs38DH.fa -s dna00001 < test.var > /dev/null'
 Benchmark #1: vartovcf -r /references/hs38DH.fa -s dna00001 < test.var > /dev/null
-  Time (mean ± σ):      1.565 s ±  0.043 s    [User: 1.543 s, System: 0.019 s]
-  Range (min … max):    1.528 s …  1.679 s    10 runs
+  Time (mean ± σ):     174.7 ms ±   1.5 ms    [User: 165.7 ms, System: 8.0 ms]
+  Range (min … max):   173.2 ms … 178.2 ms    16 runs
 
 ❯ hyperfine --warmup 5 'var2vcf_valid.pl -N dna00001 -f 0.0 -E < test.var > /dev/null'
 Benchmark #1: var2vcf_valid.pl -N dna00001 -f 0.0 -E < test.var > /dev/null
-  Time (mean ± σ):      1.815 s ±  0.021 s    [User: 1.680 s, System: 0.128 s]
-  Range (min … max):    1.789 s …  1.848 s    10 runs
+  Time (mean ± σ):     359.4 ms ±   2.5 ms    [User: 329.2 ms, System: 25.8 ms]
+  Range (min … max):   356.1 ms … 363.6 ms    10 runs
 ```