Add FASTA->2bit conversion step #76.

- remove (old) generated data files
GooglingTheCancerGenome · Nov 25, 2020 · dad6945 · dad6945
1 parent f14c3dd
commit dad6945
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Showing 8 changed files with 6 additions and 19,372 deletions.
diff --git a/data/delly.bedpe b/data/delly.bedpe
diff --git a/data/gridss.bedpe b/data/gridss.bedpe
diff --git a/data/lumpy.bedpe b/data/lumpy.bedpe
diff --git a/data/manta.bedpe b/data/manta.bedpe
diff --git a/data/reference_N_regions.bed b/data/reference_N_regions.bed
diff --git a/data/test.2bit b/data/test.2bit
diff --git a/data/test.bw b/data/test.bw
diff --git a/run.sh b/run.sh
@@ -82,6 +82,12 @@ eval "$(conda shell.bash hook)"
 conda activate $CONDA_ENV
 conda list
 
+# convert input FASTA to 2bit
+p=faToTwoBit
+cmd="$p \"$FASTA\" \"$TWOBIT\""
+JOB_ID=$(submit "$cmd" "$p")
+JOBS+=($JOB_ID)
+
 # compute genome mappability
 p=genmap
 cmd="./$p.sh \"$FASTA\" \"$BIGWIG\" $KMERS $MAX_MISMATCH"