Add step to write *.2bit & *.bed files #76.

run.sh

@@ -82,6 +82,14 @@ eval "$(conda shell.bash hook)"
 conda activate $CONDA_ENV
 conda list
 
+# extract N's from sequence into BED
+cd scripts/utils
+p=Ns_to_bed
+cmd="faToTwoBit \"$FASTA\" \"$TWOBIT\" && \
+  python $p.py -b \"$REF_REG\" -t \"$TWOBIT\" -c \"$SEQ_IDS\""
+JOB_ID=$(submit "$cmd" "$p")
+JOBS+=($JOB_ID)
+
 # compute genome mappability
 p=genmap
 cmd="./$p.sh \"$FASTA\" \"$BIGWIG\" $KMERS $MAX_MISMATCH"
@@ -110,7 +118,7 @@ cmd="python $p.py \
   -o $p.json.gz \
   -p . \
   -l $p.log"
-JOB_ID=$(submit "$cmd" $p)
+JOB_ID=$(submit "$cmd" "$p")
 JOBS+=($JOB_ID)
 
 p=clipped_read_pos
@@ -120,7 +128,7 @@ cmd="python $p.py \
   -o $p.json.gz \
   -p . \
   -l $p.log"
-JOB_ID=$(submit "$cmd" $p)
+JOB_ID=$(submit "$cmd" "$p")
 JOBS+=($JOB_ID)
 
 p=split_reads
@@ -131,7 +139,7 @@ cmd="python $p.py \
   -ob $p.bedpe.gz \
   -p . \
   -l $p.log"
-JOB_ID=$(submit "$cmd" $p)
+JOB_ID=$(submit "$cmd" "$p")
 JOBS+=($JOB_ID)
 
 for s in $(echo "$SEQ_IDS" | tr ',' ' '); do  # per chromosome