diff --git a/src/AlnDBG b/src/AlnDBG index a32c635..19059cb 160000 --- a/src/AlnDBG +++ b/src/AlnDBG @@ -1 +1 @@ -Subproject commit a32c6356671a30df729e27de5efdb53b9f073837 +Subproject commit 19059cbf53b85e47b548979c0b2b8d33ef1bda7b diff --git a/src/Snakefiles/1-buildGraph.sm b/src/Snakefiles/1-buildGraph.sm index 5baea94..51fceb5 100644 --- a/src/Snakefiles/1-buildGraph.sm +++ b/src/Snakefiles/1-buildGraph.sm @@ -48,7 +48,8 @@ rule buildGraph: baseK = config['chunkgraph_baseK'], window = config['chunkgraph_window'], - hap_coverage = config['chunkgraph_hap_coverage'] + hap_coverage = config['chunkgraph_hap_coverage'], + resolve_size = config['chunkgraph_resolve_size'] threads: int(config['chg_n_cpus']) resources: @@ -94,6 +95,7 @@ echo "" -t {resources.n_cpus} \\\\ -k {params.baseK} \\\\ -w {params.window} \\\\ + -r {params.resolve_size} \\\\ --max-error-rate 0.03 \\\\ --avg-hap-coverage {params.hap_coverage} diff --git a/src/verkko.sh b/src/verkko.sh index 7e9cb18..70d73f1 100755 --- a/src/verkko.sh +++ b/src/verkko.sh @@ -294,6 +294,7 @@ cor_overlap_batches=32 chunkgraph_baseK=11 chunkgraph_window=5000 chunkgraph_hap_coverage=20 +chunkgraph_resolve_size=10000 # buildGraph, parameters for MBG mbg_baseK=1001 mbg_maxK=15000 @@ -619,6 +620,7 @@ while [ $# -gt 0 ] ; do elif [ "$opt" = "--chunkgraph-base-k" ] ; then chunkgraph_baseK=$arg; shift elif [ "$opt" = "--chunkgraph-window" ] ; then chunkgraph_window=$arg; shift elif [ "$opt" = "--chunkgraph-hap-coverage" ] ; then chunkgraph_hap_coverage=$arg; shift + elif [ "$opt" = "--chunkgraph-resolve-size" ] ; then chunkgraph_resolve_size=$arg; shift # # MBG options @@ -1252,6 +1254,7 @@ echo >> ${outd}/verkko.yml "# build-graph, chunkgraph" echo >> ${outd}/verkko.yml "chunkgraph_baseK: '${chunkgraph_baseK}'" echo >> ${outd}/verkko.yml "chunkgraph_window: '${chunkgraph_window}'" echo >> ${outd}/verkko.yml "chunkgraph_hap_coverage: '${chunkgraph_hap_coverage}'" +echo >> ${outd}/verkko.yml "chunkgraph_resolve_size: '${chunkgraph_resolve_size}'" echo >> ${outd}/verkko.yml "# build-graph, MBG" echo >> ${outd}/verkko.yml "mbg_baseK: '${mbg_baseK}'" echo >> ${outd}/verkko.yml "mbg_maxK: '${mbg_maxK}'"