4d29ce62c5c76ed62d132f9e2ed05cfa61f7fc1a hiram Fri Sep 16 10:04:48 2022 -0700 can not use bare dollar sign in html text causes confusion for trackDb make refs #30012 diff --git src/hg/utils/automation/asmHubWindowMasker.pl src/hg/utils/automation/asmHubWindowMasker.pl index 55631a6..8202415 100755 --- src/hg/utils/automation/asmHubWindowMasker.pl +++ src/hg/utils/automation/asmHubWindowMasker.pl @@ -49,34 +49,34 @@ This track depicts masked sequence as determined by WindowMasker on the the $assemblyDate $em${organism}$noEm/$asmId/$ncbiAssemblyId genome assembly. The WindowMasker tool is included in the NCBI C++ toolkit. The source code for the entire toolkit is available from the NCBI FTP site.

Methods

To create this track, WindowMasker was run with the following parameters:

 windowmasker -mk_counts true -input $asmId.unmasked.fa -output wm_counts
 windowmasker -ustat wm_counts -sdust true -input $asmId.unmasked.fa -output windowmasker.intervals
-perl -wpe 'if (s/^>lcl\\|(.*)\\n\$//) { \$chr = \$1; } \\
+perl -wpe 'if (s/^>lcl\\|(.*)\\n$//) { $chr = $1; } \\
    if (/^(\\d+) - (\\d+)/) { \\
-   \$s=\$1; \$e=\$2+1; s/(\\d+) - (\\d+)/\$chr\\t\$s\\t\$e/; \
-   }' windowmasker.intervals > windowmasker.sdust.bed
+   $s=$1; $e=$2+1; s/(\\d+) - (\\d+)/$chr\\t$s\\t$e/; \
+   }' windowmasker.intervals > windowmasker.sdust.bed

The windowmasker.sdust.bed included masking for areas of the assembly that are gap. The file was 'cleaned' to remove those areas of masking in gaps, leaving only the sequence masking. The final result covers $basesCovered bases in the assembly size $asmSize for a percent coverage of % $percentCoverage.

References

Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41.