Added updated build command to the go.sh script

broadinstitute · Jun 14, 2024 · 96f2268 · 96f2268
1 parent a645edd
commit 96f2268
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/go.sh b/go.sh
@@ -2,7 +2,7 @@
 
 set -euxo pipefail
 
-cargo build --release >/dev/null 2>&1
+cargo build --release
 
 ./target/release/hidive fetch \
 	-r \
@@ -22,10 +22,10 @@ cargo build --release >/dev/null 2>&1
 	-o HG02559.HLA-A.bam \
 	gs://fc-bb12940d-f7ba-4515-8a98-42de84f63c34/HPRC_grch38/PBCCSWholeGenome/HG02559/alignments/HG02559.bam
 
-samtools fasta HG002.HLA-A.bam | sed '/^>/s/$/\|HG002/' > HG002.HLA-A.fasta
+samtools fasta HG002.HLA-A.bam   | sed '/^>/s/$/\|HG002/' > HG002.HLA-A.fasta
 samtools fasta HG00438.HLA-A.bam | sed '/^>/s/$/\|HG00438/' > HG00438.HLA-A.fasta
 samtools fasta HG02559.HLA-A.bam | sed '/^>/s/$/\|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
+./target/release/hidive build -l chr6:29,940,532-29,947,870 -o HLA-A.gfa HLA-A.fasta GCA_000001405.15_GRCh38_no_alt_analysis_set.fa