diff --git a/Cargo.lock b/Cargo.lock index ebfc5e10..706b9b82 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1602,7 +1602,7 @@ checksum = "7f24254aa9a54b5c858eaee2f5bccdb46aaf0e486a595ed5fd8f86ba55232a70" [[package]] name = "hidive" -version = "0.1.3" +version = "0.1.4" dependencies = [ "anyhow", "bio", @@ -3369,7 +3369,7 @@ dependencies = [ [[package]] name = "skydive" -version = "0.1.3" +version = "0.1.4" dependencies = [ "anyhow", "backoff", diff --git a/go.sh b/go.sh index 34af3b35..ae9cbb9e 100644 --- a/go.sh +++ b/go.sh @@ -4,10 +4,26 @@ set -euxo pipefail cargo build --release >/dev/null 2>&1 -./target/debug/hidive fetch \ +./target/release/hidive fetch \ -r \ - -o HG002.HLA-A.bam \ -l chr6:29,940,532-29,947,870 \ + -o HG002.HLA-A.bam \ gs://fc-bb12940d-f7ba-4515-8a98-42de84f63c34/HPRC_grch38/PBCCSWholeGenome/HG002/alignments/HG002.bam -samtools index HG002.HLA-A.bam +./target/release/hidive fetch \ + -r \ + -l chr6:29,940,532-29,947,870 \ + -o HG00438.HLA-A.bam \ + gs://fc-bb12940d-f7ba-4515-8a98-42de84f63c34/HPRC_grch38/PBCCSWholeGenome/HG00438/alignments/HG00438.bam + +./target/release/hidive fetch \ + -r \ + -l chr6:29,940,532-29,947,870 \ + -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/$/\|HG002/' > HG002.HLA-A.fasta +samtools fasta HG00438.HLA-A.bam | sed '/^>/s/$/\|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