20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,52 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+
+
+my $usage = "usage: $0 genome.fasta  left.fq  right.fq [output_dir]\n\n";
+
+my $genome_file = $ARGV[0] or die $usage;
+my $left_fq_file = $ARGV[1] or die $usage;
+my $right_fq_file = $ARGV[2] or die $usage;
+my $output_dir = $ARGV[3] || "bowtie.$$.dir";
+
+while ($output_dir =~ m|/$|) {
+    chop $output_dir;
+}
+
+
+main: {
+
+    ## run bowtie
+    my $cmd = "$FindBin::RealBin/../alignReads.pl --target $genome_file --left $left_fq_file --right $right_fq_file "
+        . " --seqType fq --aligner bowtie -o $output_dir  --max_dist_between_pairs 900000000 --no_rsem --retain_intermediate_files "
+        . " -- -a -m 1 --best --strata -p 4 --chunkmbs 512 ";
+    &process_cmd($cmd) unless (-s "$output_dir/$output_dir.nameSorted.sam");
+
+    $cmd = "$FindBin::RealBin/HiCpipe_nameSortedSam_to_raw.pl $output_dir/$output_dir.nameSorted.sam > $output_dir/$output_dir.raw";
+    &process_cmd($cmd) unless (-s "$output_dir/$output_dir.raw");
+    
+
+    exit(0);
+
+
+}
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+
+    my $ret = system($cmd);
+
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+
+    return;
+}