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Progetto di ASD per l'a.a. 2023/2024 su pangenome graphs
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Antonio De Lucreziis f0e93e92a2 updated readme 3 weeks ago
dataset some experiments 6 months ago
examples more compact 3 weeks ago
src chore: more refactoring for the graph module 3 weeks ago
.gitignore initial commit 6 months ago
001.log some progress 3 weeks ago
002.log some progress 3 weeks ago
003.log did some runs 3 weeks ago
004.log did some runs 3 weeks ago
Cargo.lock some progress 3 weeks ago
Cargo.toml some progress 3 weeks ago
README.md updated readme 3 weeks ago

README.md

Progetto ASD 2023/2024

Usage

  • cargo run -- --help

    Display help message.

  • cargo run -- show -i ./dataset/example.gfa

    Parses the GFA file and prints the graph and various information.

  • Visualize the graph using EGUI, go to examples/configurable and run:

    cargo run -- ../../dataset/example.gfa

    cargo run -- ../../dataset/DRB1-3123_unsorted.gfa

  • Running the project with all the flags:

    cargo run --release -- show -i dataset/chrX.hprc-v1.0-pggb.local.gfa -c 2 -p ACGT -k 3

Example GFA

H	VN:Z:1.0
S	11	G
S	12	A
S	13	T
S	14	T
S	15	A
S	16	C
S	17	A
S	21	G
S	22	A
S	23	T
S	24	T
S	25	A
L	11	+	12	+	*
L	11	+	13	+	*
L	12	+	14	+	*
L	13	+	14	+	*
L	14	+	15	+	*
L	14	+	16	+	*
L	15	+	17	+	*
L	16	+	17	+	*
L	21	+	22	+	*
L	21	+	23	+	*
L	22	+	24	+	*
L	23	+	24	-	*
L	24	+	25	+	*
P	A	11+,12+,14+,15+,17+	*,*,*,*
P	B	21+,22+,24+,25+	*,*,*
W	sample	1	A	0	5	>11>12>14>15>17
W	sample	2	A	0	5	>11>13>14>16>17
W	sample	1	B	0	5	>21>22>24<23<21
W	sample	2	B	0	4	>21>22>24>25

Note