704efd7a1be11b0d69aff4a9101f87ed5b62734d
angie
  Thu Jan 23 10:10:10 2020 -0800
Add NC_012920 (rCRS) mitochondrion to hg19 as chrMT.  refs #24648

diff --git src/hg/makeDb/doc/hg19.patchUpdate.13.txt src/hg/makeDb/doc/hg19.patchUpdate.13.txt
index 53684ad..b5fd706 100644
--- src/hg/makeDb/doc/hg19.patchUpdate.13.txt
+++ src/hg/makeDb/doc/hg19.patchUpdate.13.txt
@@ -145,44 +145,55 @@
     rm -rf chroms && mkdir chroms && cd chroms
     tar xvzf ../chromFa.tar.gz
     cd ..
     faSplit byname /hive/data/genomes/grcH37P13/goldenPath/bigZips/grcH37P13.fa.gz chroms/
     ls -1 chroms | wc -l
 #297
     tar cvzf p13/hg19.p13.chromFa.tar.gz ./chroms
     rm -rf chroms
 
     # Per-chrom hard-masked FASTA:
     rm -rf maskedChroms && mkdir maskedChroms && cd maskedChroms
     tar xvzf ../chromFaMasked.tar.gz
     cd ..
     faSplit byname /hive/data/genomes/grcH37P13/goldenPath/bigZips/grcH37P13.fa.masked.gz \
       maskedChroms/
+# NOTE FOR NEXT TIME: fix up names, .fa --> .fa.masked like this:
+    cd maskedChroms
+    for f in *.fa; do
+      mv $f $f.masked
+    done
+    cd ..
+# END NEXT TIME
+
     ls -1 maskedChroms | wc -l
 #297
     tar cvzf p13/hg19.p13.chromFaMasked.tar.gz ./maskedChroms
     rm -rf maskedChroms
 
     # Per-chrom RepeatMasker .out:
     rm -rf out && mkdir out && cd out
     tar xvzf ../chromOut.tar.gz
     zcat /hive/data/genomes/grcH37P13/goldenPath/bigZips/grcH37P13.fa.out.gz \
     | head -3 > RepeatMaskerHeader.txt
     zcat /hive/data/genomes/grcH37P13/goldenPath/bigZips/grcH37P13.fa.out.gz \
     | tail -n +4 \
     | splitFileByColumn -col=5 -chromDirs -head=RepeatMaskerHeader.txt -ending=.out \
       stdin .
+# NOTE FOR NEXT TIME: clean up this file:
+    rm RepeatMaskerHeader.txt
+# END NEXT TIME
     tar cvzf ../p13/hg19.p13.chromOut.tar.gz *
     cd ..
     rm -r out
 
     # Per-chrom TRF output:
     rm -rf trfMaskChrom
     tar xvzf chromTrf.tar.gz
     cd trfMaskChrom
     splitFileByColumn -ending=.bed \
       /hive/data/genomes/grcH37P13/goldenPath/bigZips/grcH37P13.trf.bed.gz .
     cd ..
     tar cvzf p13/hg19.p13.chromTrf.tar.gz ./trfMaskChrom
     rm -rf trfMaskChrom
 
     # RepeatMasker .align files: