# HG changeset patch
# User greg
# Date 1513606140 18000
# Node ID 1736d09a6927b5846220460ee88a5eb9ea26bbb7
# Parent  269241d4b9c8344b07a0a6b4f0a672dd6e30492e
Uploaded

diff -r 269241d4b9c8 -r 1736d09a6927 ideas_genome_tracks.R
--- a/ideas_genome_tracks.R	Mon Dec 18 07:40:15 2017 -0500
+++ b/ideas_genome_tracks.R	Mon Dec 18 09:09:00 2017 -0500
@@ -86,8 +86,10 @@
         track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed");
         x = cbind(np[, 1:3], state_name[as.integer(np[,4])+1], 1000, ".", np[,2:3]);
         write.table(as.matrix(x), track_file_name_bed_unsorted, quote=F, row.names=F, col.names=F);
-        system(paste("LC_COLLATE=C sort -k1,1 -k2,2n < ", track_file_name_bed_unsorted, " > track_file_name_bed"));
-        system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed));
+        cmd = paste("LC_COLLATE=C sort -k1,1 -k2,2n < ", track_file_name_bed_unsorted, " > ", track_file_name_bed);
+        system(cmd);
+        cmd = paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed);
+        system(cmd);
         system(paste("rm ", track_file_name_bed_unsorted));
         system(paste("rm ", track_file_name_bed));
     }