Add samtools to index FASTA #76.

GooglingTheCancerGenome · Nov 25, 2020 · 1d9d3d9 · 1d9d3d9
1 parent f8da830
commit 1d9d3d9
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/genmap.sh b/genmap.sh
@@ -18,6 +18,7 @@ INDEX="$BASE_DIR/genmap_index"
 MAP="$BASE_DIR/genmap_K${KMERS}_E${MAX_MISMATCH}"
 
 rm -fr "$INDEX" "$MAP*" "$FAI*"
+samtools faidx -o "$FAI" "$FASTA"
 genmap index -F "$FASTA" -I "$INDEX"
 genmap map -K "$KMERS" -E "$MAX_MISMATCH" -I "$INDEX" -O "$MAP" -bg
 cut -f 1,2 "$FAI" > "$FAI.sizes"