Merge pull request #454 from pangenome/update_defaul_g

Two rounds of smoothing by default

Author: AndreaGuarracino

Dockerfile

@@ -77,7 +77,7 @@ RUN git clone --recursive https://github.com/ekg/seqwish \
 RUN git clone --recursive https://github.com/pangenome/smoothxg \
     && cd smoothxg \
     && git pull \
-    && git checkout 1182e148de177e7878c7407633332df235a1e90a \
+    && git checkout 6a2193db950acd6b2d77c265d6e1faa66944238e \
     && git submodule update --init --recursive \
     && sed -i 's/-msse4.1/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \
     && sed -i 's/-march=native/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \

README.md

@@ -73,13 +73,13 @@ pggb -i output/in.fa.dd9e519.community.0.fa \
      -o output/in.fa.dd9e519.community.0.fa.out \
      -p 5k -l 25000 -p 90 -n 9 -K 19 -F 0.001 \
      -k 19 -f 0 -B 10000000 \
-     -H 9 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \
+     -H 9 -j 0 -e 0 -G 700,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \
      -V ref:1000 --threads 16 --poa-threads 16
 pggb -i output/in.fa.dd9e519.community.1.fa \
      -o output/in.fa.dd9e519.community.1.fa.out \
      -p 5k -l 25000 -p 90 -n 9 -K 19 -F 0.001 \
      -k 19 -f 0 -B 10000000 \
-     -H 9 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \
+     -H 9 -j 0 -e 0 -G 700,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \
      -V ref:1000 --threads 16 --poa-threads 16
 ```
 

docs/rst/quick_start.rst

@@ -78,13 +78,13 @@ This generates the command lines to run ``pggb`` on each community (2 in this ex
          -o output/in.fa.dd9e519.community.0.fa.out \
          -p 5k -l 25000 -p 90 -n 9 -K 19 -F 0.001 \
          -k 19 -f 0 -B 10000000 \
-         -H 9 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \
+         -H 9 -j 0 -e 0 -G 700,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \
          -V ref:1000 --threads 16 --poa-threads 16
     pggb -i output/in.fa.dd9e519.community.1.fa \
          -o output/in.fa.dd9e519.community.1.fa.out \
          -p 5k -l 25000 -p 90 -n 9 -K 19 -F 0.001 \
          -k 19 -f 0 -B 10000000 \
-         -H 9 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \
+         -H 9 -j 0 -e 0 -G 700,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \
          -V ref:1000 --threads 16 --poa-threads 16
 
 

partition-before-pggb

@@ -36,7 +36,7 @@ transclose_batch=$TRANSCLOSE_BATCH
 # smoothxg's default values
 MAX_PATH_JUMP=0
 MAX_EDGE_JUMP=0
-TARGET_POA_LENGTH=700,900,1100
+TARGET_POA_LENGTH=700,1100
 POA_PADDING=0.001
 PAD_MAX_DEPTH=100
 CONSENSUS_PREFIX=Consensus_

pggb

@@ -36,7 +36,7 @@ transclose_batch=$TRANSCLOSE_BATCH
 # smoothxg's default values
 MAX_PATH_JUMP=0
 MAX_EDGE_JUMP=0
-TARGET_POA_LENGTH=700,900,1100
+TARGET_POA_LENGTH=700,1100
 POA_PADDING=0.001
 PAD_MAX_DEPTH=100
 CONSENSUS_PREFIX=Consensus_