preparing patch

Author: ACEnglish

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "kanpig"
-version = "0.1.2-dev"
+version = "0.1.2"
 edition = "2021"
 
 [dependencies]

changelog.md

@@ -1,9 +1,14 @@
 v0.1.2
-*in progress*
+*May 5, 2024*
 
-* IO improvements: Off-loaded annotation work from the single writer thread to the worker threads and using a large
-  multiple of page size for the BufWriter capacity
+* New optional hompolymer filter doesn't kmerize long homopolymers
 * Improved logging info
+* Correcting GQ field
+* Correcting kmer counting
+* Small speed/memory/io improvements
+  * Off-loaded annotation work from the single writer thread to the worker threads and using a large
+  multiple of page size for the BufWriter capacity
+  * Fewer bam file opens
 
 v0.1.1
 *Apr 11, 2024*

experiments/bedtest.sh

@@ -10,7 +10,7 @@ create() {
         --sizemin 50 \
         --sizesim 0.95 --seqsim 0.90 --threads 4 \
         --maxpaths 10000 --mapq 5 --hapsim 0.98 \
-        --chunksize 100 --maxhom 0 \
+        --chunksize 100 --maxhom 5 \
         -o test_rs/hc.vcf --bed $bed 
     # --bed /Users/english/code/kanpig/test/GRCh38_HG002-T2TQ100-V1.0_stvar.benchmark.bed \
     # --bam /Users/english/code/kanpig/experiments/test_rs/GIABHG002.bam \