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make temp dir more robust #349

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make temp dir more robust #349

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0bd3609
make temp dir more robust
y9c Feb 14, 2022
753f53f
Merge branch 'DaehwanKimLab:hisat-3n' into hisat-3n
y9c Feb 25, 2022
aea25e5
Update position_3n_table.h
y9c Feb 25, 2022
517427a
Update position_3n_table.h
y9c Feb 25, 2022
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2 changes: 1 addition & 1 deletion hisat-3n
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Original file line number Diff line number Diff line change
Expand Up @@ -287,7 +287,7 @@ my @mate1s = ();
my @mate2s = ();
my @to_delete = ();
my @to_kills = ();
my $temp_dir = "/tmp";
my $temp_dir = File::Spec->tmpdir();
my $bam_out = 0;
my $ref_str = undef;
my $no_pipes = 0;
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2 changes: 1 addition & 1 deletion position_3n_table.h
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Expand Up @@ -239,7 +239,7 @@ class Positions{
* this is important when there is space in chromosome name. the SAM information only contain the first word.
*/
string getChrName(string& inputLine) {
size_t endPosition = inputLine.find(' ', 0);
size_t endPosition = inputLine.find_first_of(" \t");
string name = inputLine.substr(1, endPosition-1);

if(removedChrName) {
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