First version of build command

broadinstitute · Jun 13, 2024 · 82f90f5 · 82f90f5
1 parent ffd72cd
commit 82f90f5
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Showing 5 changed files with 556 additions and 8 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/go.sh b/go.sh
@@ -27,3 +27,5 @@ samtools fasta HG00438.HLA-A.bam | sed '/^>/s/$/\|HG00438/' > HG00438.HLA-A.fast
 samtools fasta HG02559.HLA-A.bam | sed '/^>/s/$/\|HG02559/' > HG02559.HLA-A.fasta
 
 cat HG002.HLA-A.fasta HG00438.HLA-A.fasta HG02559.HLA-A.fasta > HLA-A.fasta
+
+./target/release/hidive build HLA-A.fasta GCA_000001405.15_GRCh38_no_alt_analysis_set.fa
diff --git a/src/hidive/Cargo.toml b/src/hidive/Cargo.toml
@@ -11,6 +11,7 @@ anyhow = "1.0"
 bio = "*"
 clap = { version = "4.5.1", features = ["derive"] }
 eyre = "0.6.8"
+flate2 = "*"
 needletail = "*"
 noodles = "*"
 path-absolutize = "3.1.1"
@@ -21,6 +22,7 @@ petgraph = "*"
 rayon = "*"
 regex = "*"
 rust-htslib = { version = "*", features = ["gcs", "serde_feature"] }
+serde = "*"
 serde_json = "*"
 skydive = { path = "../skydive" }
 url = "*"
Original file line number	Diff line number	Diff line change
Expand Up		@@ -27,3 +27,5 @@ samtools fasta HG00438.HLA-A.bam \| sed '/^>/s/$/\\|HG00438/' > HG00438.HLA-A.fast
		samtools fasta HG02559.HLA-A.bam \| sed '/^>/s/$/\\|HG02559/' > HG02559.HLA-A.fasta

		cat HG002.HLA-A.fasta HG00438.HLA-A.fasta HG02559.HLA-A.fasta > HLA-A.fasta

		./target/release/hidive build HLA-A.fasta GCA_000001405.15_GRCh38_no_alt_analysis_set.fa