trim-graph

Simple tool to remove segments/links/jumps from GFA files that are not covered by any paths/walks.

To build:

cargo build --release

To run:

./target/release/trim-graph ${GFA_FILE}

trim-graph can also be set to keep only certain paths (+ all their segments/links). For this one needs to have a file containing all the paths that should be kept, one per line.

./target/release/trim-graph ${GFA_FILE} --paths_to_keep=${PATHS_FILE}

While walks are supported by trim-graph, it currently has no parameters to only keep certain walks. Thus, to remove a certain group of walks use another tool (e.g. sed '/W\tHG00741/d' to remove all walks of sample HG00741) to remove the walks and then run trim-graph on the modified graph to trim off the segments/links that are not covered anymore.

Jump lines are also supported and are distinguished from links: if only jumps from segment 11 to segment 12 are used and no links, the links from segment 11 to 12 will be removed (and also vice versa).