<commit_before>package Sam2BamSorted;

use strict;
use warnings;
use File::Basename;

# Convert SAM to BAM
sub sam2Bam 
{
   # XXX fix the VREGION argument
   my @VREGION = ();
   my ($VIEWFLAG, $REFERENCE, $SAMFILE) = @_;
   my ($name,$path,$suffix) = fileparse($SAMFILE, ".sam");
   my $BAMALIGN = $path."Binary/".$name.".bam";
   my $COMM = "samtools view $VIEWFLAG -t $REFERENCE.fai -o $BAMALIGN $SAMFILE @VREGION";

   print "Converting to BAM\n";<commit_msg>Added comment about Binary directory assumption.<commit_after>package Sam2BamSorted;

use strict;
use warnings;
use File::Basename;

# Convert SAM to BAM
# Assumes the Binary directory has been created already.
sub sam2Bam 
{
   # XXX fix the VREGION argument
   my @VREGION = ();
   my ($VIEWFLAG, $REFERENCE, $SAMFILE) = @_;
   my ($name,$path,$suffix) = fileparse($SAMFILE, ".sam");
   my $BAMALIGN = $path."Binary/".$name.".bam";
   my $COMM = "samtools view $VIEWFLAG -t $REFERENCE.fai -o $BAMALIGN $SAMFILE @VREGION";

   print "Converting to BAM\n";
{'fraction_non_alphanumeric': 0.1480392156862745, 'fraction_numerical': 0.00392156862745098, 'mean_word_length': 4.130653266331659, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3265968', 'n_tokens_mistral': 380, 'n_tokens_neox': 373, 'n_words': 106}