From f1b1952d1460f3707dbd248819c0cded46b04852 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Tue, 13 Aug 2024 12:28:35 -0700
Subject: [PATCH 1/3] Allow preparing a local chunk to produce a BED path from
 somewhere other than the current directory

---
 scripts/prepare_local_chunk.sh | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/scripts/prepare_local_chunk.sh b/scripts/prepare_local_chunk.sh
index 63d813c5..5f5a3c53 100755
--- a/scripts/prepare_local_chunk.sh
+++ b/scripts/prepare_local_chunk.sh
@@ -4,7 +4,7 @@ set -e
 function usage() {
     echo >&2 "${0}: Prepare a tube map chunk and BED line on standard output from a pre-made subgraph. Only supports paths, not haplotypes."
     echo >&2
-    echo >&2 "Usage: ${0} -x subgraph.xg -r chr1:1-100 [-d 'Description of region'] [-n 123 [-n 456]] -o chunk-chr1-1-100 [-g mygam1.gam [-p '{\"mainPalette\": \"blues\", \"auxPalette\": \"reds\"}'] [-g mygam2.gam [-p ...] ...]] >> regions.bed"
+    echo >&2 "Usage: ${0} -x subgraph.xg -r chr1:1-100 [-d 'Description of region'] [-n 123 [-n 456]] -o chunk-chr1-1-100 [-g mygam1.gam [-p '{\"mainPalette\": \"blues\", \"auxPalette\": \"reds\"}'] [-g mygam2.gam [-p ...] ...]] [-b /output/directory/prefix/to/remove] >> regions.bed"
     exit 1
 }
 
@@ -20,6 +20,7 @@ do
         p) GAM_PALETTES+=("$OPTARG");;
         r) REGION="${OPTARG}";;
         o) OUTDIR="${OPTARG}";;
+        b) BASEDIR="${OPTARG}";;
         d) DESC="${OPTARG}";;
         n) NODE_COLORS+=("${OPTARG}");;
         *)
@@ -53,6 +54,12 @@ if [[ -z "${OUTDIR}" ]] ; then
     usage
 fi
 
+if [[ ! -z "${BASEDIR}" && "${OUTDIR}" != "${BASEDIR}"* ]] ; then
+    echo >&2 "Base directory from -b is not a prefix of out directory from -o"
+    echo >&2
+    usage
+fi
+
 if [[ -z "${DESC}" ]] ; then
     DESC="Region ${REGION}"
 fi
@@ -146,9 +153,16 @@ do
     printf "$file\n" >> "$OUTDIR/chunk_contents.txt"
 done
 
+# Work out how the BED should refer to the OUTDIR
+PATH_TO_OUTDIR="${OUTDIR}"
+if [[ ! -z "${BASEDIR}" ]] ; then
+    # Remove BASEDIR from the front of OUTDIR
+    PATH_TO_OUTDIR="${OUTDIR#"$BASEDIR"}"
+fi
+
 # Print BED line
 cat "$OUTDIR/regions.tsv" | cut -f1-3 | tr -d "\n"
-printf "\t${DESC}\t${OUTDIR}\n"
+printf "\t${DESC}\t${PATH_TO_OUTDIR}\n"
 
 rm -fr "$TEMP"
 

From 432c7d2069144f5dd54e6d839e6d3e96600c132a Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Tue, 13 Aug 2024 12:31:02 -0700
Subject: [PATCH 2/3] Require trailing slash

---
 scripts/prepare_local_chunk.sh | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/scripts/prepare_local_chunk.sh b/scripts/prepare_local_chunk.sh
index 5f5a3c53..d7b09e56 100755
--- a/scripts/prepare_local_chunk.sh
+++ b/scripts/prepare_local_chunk.sh
@@ -60,6 +60,12 @@ if [[ ! -z "${BASEDIR}" && "${OUTDIR}" != "${BASEDIR}"* ]] ; then
     usage
 fi
 
+if [[ ! -z "${BASEDIR}" && "${BASEDIR}" != *"/" ]] ; then
+    echo >&2 "Base directory from -b does not end with a slash"
+    echo >&2
+    usage
+fi
+
 if [[ -z "${DESC}" ]] ; then
     DESC="Region ${REGION}"
 fi

From e1045379c854aecb8f5b0c9f19af2413f7108bee Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Tue, 13 Aug 2024 12:36:56 -0700
Subject: [PATCH 3/3] Note b option existence for option parsing

---
 scripts/prepare_local_chunk.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/prepare_local_chunk.sh b/scripts/prepare_local_chunk.sh
index d7b09e56..c1f27a44 100755
--- a/scripts/prepare_local_chunk.sh
+++ b/scripts/prepare_local_chunk.sh
@@ -12,7 +12,7 @@ GAM_FILES=()
 GAM_PALETTES=()
 NODE_COLORS=()
 
-while getopts x:g:p:r:o:d:n: flag
+while getopts x:g:p:r:o:b:d:n: flag
 do
     case "${flag}" in
         x) GRAPH_FILE="${OPTARG}";;