new chunkgraph version

marbl · Jan 6, 2025 · 8eb3988 · 8eb3988
1 parent fbcee95
commit 8eb3988
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Showing 2 changed files with 3 additions and 5 deletions.
diff --git a/src/AlnDBG b/src/AlnDBG
diff --git a/src/Snakefiles/1-buildGraph.sm b/src/Snakefiles/1-buildGraph.sm
@@ -99,11 +99,9 @@ echo ""
   --max-error-rate 0.03 \\\\
   --avg-hap-coverage {params.hap_coverage}
 
-cp graph-fragmented-final.gfa ../{output.graph}
+cp graph-resolved-final.gfa ../{output.graph}
 
-# todo fix: chunkgraph path unitig positions are currently not always correct.
-# fix the ones which have impossible positions and ignore the ones which have incorrect but possible positions
-awk 'BEGIN{{FS="\\t";OFS="\\t"}}{{if (\$8 > \$7) {{\$8 = 0;}} if (\$9 > \$7) {{\$9 = \$7;}} if (\$8 < \$9) {{print;}} }}' < paths-fragmented-final.gaf > ../{output.paths}
+cp paths-resolved-final.gaf ../{output.paths}
 
 #  Find coverage.
 #    (rule hifi_coverage_csv in the original Snakefile)
+6 −2		src/ChunkGraphWriter.cpp
+735 −6		src/ChunkPhasing.cpp
+1 −0		src/ChunkPhasing.h
+270 −183		src/ChunkUnitigGraph.cpp
+1 −1		src/ChunkUnitigGraph.h
+42 −3		src/KmerIterator.cpp
+35 −2		src/TransitiveClosure.h
+19 −0		src/UnionFind.cpp
+2 −0		src/UnionFind.h
+351 −9		src/chunkgraph.cpp