[med-svn] [gmap] 01/03: Imported Upstream version 2015-12-31.v8
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Feb 26 13:37:09 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 4c0bafddf60ffb47c49b673691d34e923d30123c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Feb 26 12:03:19 2016 +0100
Imported Upstream version 2015-12-31.v8
---
ChangeLog | 14 ++++
src/stage3hr.c | 177 ++++++++++++++++++++++++++------------------------
src/substring.c | 20 +++---
util/gmap_build.pl.in | 35 +++++-----
4 files changed, 135 insertions(+), 111 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index c2032b1..37cee49 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,17 @@
+2016-02-18 twu
+
+ * stage3hr.c: Applied revision 184528 from trunk to check for stage2pairs
+ being NULL
+
+ * gmap_build.pl.in: Applied revision 184521 from trunk to add quotes around
+ bindir programs
+
+ * stage3hr.c: Applied revision 184518 from trunk to fix creating stage 2
+ pairs for circular chromosomes
+
+ * substring.c: Fixed overflow bug from using this->genomiclength instead of
+ querylength
+
2016-02-04 twu
* stage2.c: Fixed termination condition for while loop
diff --git a/src/stage3hr.c b/src/stage3hr.c
index fc15b26..03a1e21 100644
--- a/src/stage3hr.c
+++ b/src/stage3hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage3hr.c 182190 2016-01-12 22:51:09Z twu $";
+static char rcsid[] = "$Id: stage3hr.c 184529 2016-02-18 19:28:56Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -5341,53 +5341,57 @@ Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
}
}
- knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
- stage2pairs = List_reverse(stage2pairs);
- knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
-
- if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
- &matches,&nmatches_posttrim,&max_match_length,
- &ambig_end_length_5,&ambig_end_length_3,
- &ambig_splicetype_5,&ambig_splicetype_3,
- &ambig_prob_5,&ambig_prob_3,
- &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
- &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
- stage2pairs,all_stage2_starts,all_stage2_ends,
+ if (stage2pairs == NULL) {
+ hit = (T) NULL;
+ } else {
+ knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+ stage2pairs = List_reverse(stage2pairs);
+ knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+
+ if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
+ &matches,&nmatches_posttrim,&max_match_length,
+ &ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,
+ &ambig_prob_5,&ambig_prob_3,
+ &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
+ &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
+ stage2pairs,all_stage2_starts,all_stage2_ends,
#ifdef END_KNOWNSPLICING_SHORTCUT
- cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
- watsonp ? query_compress_fwd : query_compress_rev,
+ cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
+ watsonp ? query_compress_fwd : query_compress_rev,
#endif
- /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
+ /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
#ifdef EXTRACT_GENOMICSEG
- /*query_subseq_offset*/0,
+ /*query_subseq_offset*/0,
#else
- /*query_subseq_offset*/0,
+ /*query_subseq_offset*/0,
#endif
- this->chrnum,this->chroffset,this->chrhigh,
- knownsplice_limit_low,knownsplice_limit_high,/*plusp*/true,genestrand,
- /*jump_late_p*/false,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
- /*sense_try*/0,/*sense_filter*/0,
- oligoindices_minor,diagpool,cellpool)) == NULL) {
- hit = (T) NULL;
+ this->chrnum,this->chroffset,this->chrhigh,
+ knownsplice_limit_low,knownsplice_limit_high,/*plusp*/true,genestrand,
+ /*jump_late_p*/false,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
+ /*sense_try*/0,/*sense_filter*/0,
+ oligoindices_minor,diagpool,cellpool)) == NULL) {
+ hit = (T) NULL;
- } else {
- nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
- pairarray,npairs);
- start = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
- /*minusterm*/Pair_querypos(&(pairarray[0])),this->chroffset);
- end = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
- /*plusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chrhigh);
+ } else {
+ nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
+ pairarray,npairs);
+ start = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
+ /*minusterm*/Pair_querypos(&(pairarray[0])),this->chroffset);
+ end = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
+ /*plusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chrhigh);
- if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
- ambig_end_length_5,ambig_end_length_3,
- ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
- pairarray,npairs,nsegments,nintrons,nindelbreaks,
- /*left*/start,/*genomiclength*/end - start + 1,
- /*plusp*/true,genestrand,first_read_p,
- /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
- cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
- FREE_OUT(pairarray);
+ if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
+ ambig_end_length_5,ambig_end_length_3,
+ ambig_splicetype_5,ambig_splicetype_3,
+ ambig_prob_5,ambig_prob_3,min_splice_prob,
+ pairarray,npairs,nsegments,nintrons,nindelbreaks,
+ /*left*/start,/*genomiclength*/end - start + 1,
+ /*plusp*/true,genestrand,first_read_p,
+ /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
+ cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
+ FREE_OUT(pairarray);
+ }
}
}
@@ -5558,10 +5562,10 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
querypos = Substring_querystart(substring);
seglength = Substring_queryend(substring) - querypos;
- /* Don't understand why it isn't this->chrlength - 1, but it
+ /* Don't understand why it isn't this->chrhigh - 1, but it
looks like the minus coordinates for substrings are +1 higher
than they should be */
- genomepos = (this->chrlength + 1) - Substring_alignstart_trim_chr(substring);
+ genomepos = (this->chrhigh + 1) - Substring_alignstart_trim(substring);
Genome_get_segment_blocks_right(gsequence_orig,gsequence_alt,/*left*/Substring_alignend_trim(substring),
seglength,this->chrhigh,/*revcomp*/true);
@@ -5586,54 +5590,57 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
}
}
-
- knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
- stage2pairs = List_reverse(stage2pairs);
- knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+ if (stage2pairs == NULL) {
+ hit = (T) NULL;
+ } else {
+ knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+ stage2pairs = List_reverse(stage2pairs);
+ knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
- if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
- &matches,&nmatches_posttrim,&max_match_length,
- &ambig_end_length_5,&ambig_end_length_3,
- &ambig_splicetype_5,&ambig_splicetype_3,
- &ambig_prob_5,&ambig_prob_3,
- &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
- &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
- stage2pairs,all_stage2_starts,all_stage2_ends,
+ if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
+ &matches,&nmatches_posttrim,&max_match_length,
+ &ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,
+ &ambig_prob_5,&ambig_prob_3,
+ &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
+ &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
+ stage2pairs,all_stage2_starts,all_stage2_ends,
#ifdef END_KNOWNSPLICING_SHORTCUT
- cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
- watsonp ? query_compress_fwd : query_compress_rev,
+ cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
+ watsonp ? query_compress_fwd : query_compress_rev,
#endif
- /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
+ /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
#ifdef EXTRACT_GENOMICSEG
- /*query_subseq_offset*/0,
+ /*query_subseq_offset*/0,
#else
- /*query_subseq_offset*/0,
-#endif
- this->chrnum,this->chroffset,this->chrhigh,
- knownsplice_limit_low,knownsplice_limit_high,/*plusp*/false,genestrand,
- /*jump_late_p*/true,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
- /*sense_try*/0,/*sense_filter*/0,
- oligoindices_minor,diagpool,cellpool)) == NULL) {
- hit = (T) NULL;
-
- } else {
- nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
- pairarray,npairs);
- start = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
- /*plusterm*/Pair_querypos(&(pairarray[0])),this->chrhigh);
- end = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
- /*minusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chroffset);
- if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
- ambig_end_length_5,ambig_end_length_3,
- ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
- pairarray,npairs,nsegments,nintrons,nindelbreaks,
- /*left*/end,/*genomiclength*/start - end + 1,
- /*plusp*/false,genestrand,first_read_p,
- /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
- cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
- FREE_OUT(pairarray);
+ /*query_subseq_offset*/0,
+#endif
+ this->chrnum,this->chroffset,this->chrhigh,
+ knownsplice_limit_low,knownsplice_limit_high,/*plusp*/false,genestrand,
+ /*jump_late_p*/true,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
+ /*sense_try*/0,/*sense_filter*/0,
+ oligoindices_minor,diagpool,cellpool)) == NULL) {
+ hit = (T) NULL;
+
+ } else {
+ nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
+ pairarray,npairs);
+ start = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
+ /*plusterm*/Pair_querypos(&(pairarray[0])),this->chrhigh);
+ end = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
+ /*minusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chroffset);
+ if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
+ ambig_end_length_5,ambig_end_length_3,
+ ambig_splicetype_5,ambig_splicetype_3,
+ ambig_prob_5,ambig_prob_3,min_splice_prob,
+ pairarray,npairs,nsegments,nintrons,nindelbreaks,
+ /*left*/end,/*genomiclength*/start - end + 1,
+ /*plusp*/false,genestrand,first_read_p,
+ /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
+ cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
+ FREE_OUT(pairarray);
+ }
}
}
diff --git a/src/substring.c b/src/substring.c
index c82905c..69aa9f1 100644
--- a/src/substring.c
+++ b/src/substring.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: substring.c 182190 2016-01-12 22:51:09Z twu $";
+static char rcsid[] = "$Id: substring.c 184487 2016-02-18 03:28:42Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -1043,7 +1043,7 @@ Substring_print_ends (T this, int chrnum) {
if (this == NULL) {
printf("NA ");
} else {
- printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend);
+ printf("#%d:%llu..%llu ",chrnum,(unsigned long long) this->alignstart,(unsigned long long) this->alignend);
}
return;
}
@@ -1690,7 +1690,7 @@ embellish_genomic_sam (char *genomic_diff, char *query, int querystart, int quer
if (exactp == true) {
/* No need to mark mismatches */
} else {
- for (k = 0, i = queryend, j = queryend; i < querylength && j < genomiclength; k++, i++, j++) {
+ for (k = 0, i = queryend, j = queryend; i < querylength /*&& j < genomiclength*/; k++, i++, j++) {
if (query[i] == genomic_diff[j]) {
result[i] = genomic_diff[j];
assert(result[i] == 'A' || result[i] == 'C' || result[i] == 'G' || result[i] == 'T' || result[i] == 'N');
@@ -2309,14 +2309,15 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
this->nmismatches_refdiff = 0;
} else {
+ /* Was this->genomiclength, but fails for large insertions */
#ifdef HAVE_ALLOCA
- gbuffer = (char *) ALLOCA((this->genomiclength+1) * sizeof(char));
+ gbuffer = (char *) ALLOCA((querylength+1) * sizeof(char));
#else
- if (this->genomiclength < MAX_READLENGTH) {
+ if (querylength < MAX_READLENGTH) {
gbuffer = gbuffer_alloc;
allocp = false;
} else {
- gbuffer = (char *) MALLOC((this->genomiclength+1) * sizeof(char));
+ gbuffer = (char *) MALLOC((querylength+1) * sizeof(char));
allocp = true;
}
#endif
@@ -2380,14 +2381,15 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
this->nmismatches_refdiff = 0;
} else {
+ /* Was this->genomiclength, but fails for large insertions */
#ifdef HAVE_ALLOCA
- gbuffer = (char *) ALLOCA((this->genomiclength+1) * sizeof(char));
+ gbuffer = (char *) ALLOCA((querylength+1) * sizeof(char));
#else
- if (this->genomiclength < MAX_READLENGTH) {
+ if (querylength < MAX_READLENGTH) {
gbuffer = gbuffer_alloc;
allocp = false;
} else {
- gbuffer = (char *) MALLOC((this->genomiclength+1) * sizeof(char));
+ gbuffer = (char *) MALLOC((querylength+1) * sizeof(char));
allocp = true;
}
#endif
diff --git a/util/gmap_build.pl.in b/util/gmap_build.pl.in
index 830b6a0..3bc13c0 100644
--- a/util/gmap_build.pl.in
+++ b/util/gmap_build.pl.in
@@ -1,5 +1,5 @@
#! @PERL@
-# $Id: gmap_build.pl.in 173897 2015-09-12 00:11:59Z twu $
+# $Id: gmap_build.pl.in 184522 2016-02-18 17:51:14Z twu $
use warnings;
@@ -8,13 +8,14 @@ my $package_version = "@PACKAGE_VERSION@";
use IO::File;
use File::Copy;
+#use File::Basename;
use Getopt::Long;
-Getopt::Long::Configure(qw(no_auto_abbrev no_ignore_case_always));
+Getopt::Long::Configure(qw(no_auto_abbrev no_ignore_case_always));
# Default values
-my $bindir = "@BINDIR@";
+my $bindir = "@BINDIR@"; # dirname(__FILE__)
my $sampling = 3;
my $sleeptime = 2;
@@ -174,7 +175,7 @@ $genomecompfile = compress_genome($nmessages_flag,$bindir,$dbdir,$dbname,$gmap_p
unshuffle_genome($bindir,$dbdir,$dbname,$genomecompfile);
-$index_cmd = "$bindir/gmapindex -k $kmersize -q $sampling $nmessages_flag -d $dbname -F \"$dbdir\" -D \"$dbdir\"";
+$index_cmd = "\"$bindir/gmapindex\" -k $kmersize -q $sampling $nmessages_flag -d $dbname -F \"$dbdir\" -D \"$dbdir\"";
if (count_index_offsets($index_cmd,$genomecompfile) == 1) {
$index_cmd .= " -H";
@@ -198,7 +199,7 @@ exit;
#####################################################################################
sub check_compiler_assumptions {
- if (system("$bindir/gmapindex -9") != 0) {
+ if (system("\"$bindir/gmapindex\" -9") != 0) {
print STDERR "There is a mismatch between this computer system and the one where gmapindex was compiled. Exiting.\n";
exit(9);
}
@@ -233,12 +234,12 @@ sub create_coords {
if (defined($mdfile)) {
# MD file cannot specify that a chromosome is circular
- $cmd = "$bindir/md_coords -o \"$coordsfile\" $mdfile";
+ $cmd = "\"$bindir/md_coords\" -o \"$coordsfile\" $mdfile";
} else {
if (defined($fasta_pipe)) {
- $cmd = "$fasta_pipe | $bindir/fa_coords $circular_flag $contigs_mapped_flag -o \"$coordsfile\"";
+ $cmd = "$fasta_pipe | \"$bindir/fa_coords\" $circular_flag $contigs_mapped_flag -o \"$coordsfile\"";
} else {
- $cmd = "$bindir/fa_coords $gunzip_flag $circular_flag $contigs_mapped_flag -o \"$coordsfile\"";
+ $cmd = "\"$bindir/fa_coords\" $gunzip_flag $circular_flag $contigs_mapped_flag -o \"$coordsfile\"";
}
if (defined($chrnamefile)) {
$cmd .= " -n $chrnamefile";
@@ -259,9 +260,9 @@ sub make_gmap_process_pipe {
my ($fasta_pipe, $gunzip_flag, $bindir, $coordsfile, $fasta_sources) = @_;
if (defined($fasta_pipe)) {
- return "$fasta_pipe | $bindir/gmap_process -c \"$coordsfile\"";
+ return "$fasta_pipe | \"$bindir/gmap_process\" -c \"$coordsfile\"";
} else {
- return "$bindir/gmap_process $gunzip_flag -c \"$coordsfile\" -f \"$fasta_sources\"";
+ return "\"$bindir/gmap_process\" $gunzip_flag -c \"$coordsfile\" -f \"$fasta_sources\"";
}
}
@@ -270,7 +271,7 @@ sub make_contig {
$bindir, $dbdir, $dbname, $gmap_process_pipe) = @_;
my ($cmd, $rc);
- $cmd = "$gmap_process_pipe | $bindir/gmapindex $nmessages_flag -d $dbname -D \"$dbdir\" -A $chr_order_flag";
+ $cmd = "$gmap_process_pipe | \"$bindir/gmapindex\" $nmessages_flag -d $dbname -D \"$dbdir\" -A $chr_order_flag";
print STDERR "Running $cmd\n";
if (($rc = system($cmd)) != 0) {
die "$cmd failed with return code $rc";
@@ -284,7 +285,7 @@ sub compress_genome {
my $genomecompfile = "$dbdir/$dbname.genomecomp";
my ($cmd, $rc);
- $cmd = "$gmap_process_pipe | $bindir/gmapindex $nmessages_flag -d $dbname -F \"$dbdir\" -D \"$dbdir\" -G";
+ $cmd = "$gmap_process_pipe | \"$bindir/gmapindex\" $nmessages_flag -d $dbname -F \"$dbdir\" -D \"$dbdir\" -G";
print STDERR "Running $cmd\n";
if (($rc = system($cmd)) != 0) {
die "$cmd failed with return code $rc";
@@ -297,7 +298,7 @@ sub unshuffle_genome {
my ($bindir, $dbdir, $dbname, $genomecompfile) = @_;
my ($cmd, $rc);
- $cmd = "cat \"$genomecompfile\" | $bindir/gmapindex -d $dbname -U > \"$dbdir/$dbname.genomebits128\"";
+ $cmd = "cat \"$genomecompfile\" | \"$bindir/gmapindex\" -d $dbname -U > \"$dbdir/$dbname.genomebits128\"";
print STDERR "Running $cmd\n";
if (($rc = system($cmd)) != 0) {
die "$cmd failed with return code $rc";
@@ -310,7 +311,7 @@ sub unshuffle_genome {
#sub full_ASCII_genome {
# make_contig();
#
-# $cmd = "$bindir/gmap_process $gunzip_flag -c $dbdir/$dbname.coords $genome_fasta | $bindir/gmapindex $nmessages_flag -d $dbname -F $dbdir -D $dbdir -l -G";
+# $cmd = "\"$bindir/gmap_process\" $gunzip_flag -c $dbdir/$dbname.coords $genome_fasta | \"$bindir/gmapindex\" $nmessages_flag -d $dbname -F $dbdir -D $dbdir -l -G";
# print STDERR "Running $cmd\n";
# if (($rc = system($cmd)) != 0) {
# die "$cmd failed with return code $rc";
@@ -370,7 +371,7 @@ sub make_enhanced_suffix_array {
my ($cmd, $rc);
# Suffix array
- $cmd = "$bindir/gmapindex -d $dbname -F \"$dbdir\" -D \"$dbdir\" -S";
+ $cmd = "\"$bindir/gmapindex\" -d $dbname -F \"$dbdir\" -D \"$dbdir\" -S";
print STDERR "Running $cmd\n";
if (($rc = system($cmd)) != 0) {
die "$cmd failed with return code $rc";
@@ -378,7 +379,7 @@ sub make_enhanced_suffix_array {
sleep($sleeptime);
# LCP and child arrays
- $cmd = "$bindir/gmapindex -d $dbname -F \"$dbdir\" -D \"$dbdir\" -L";
+ $cmd = "\"$bindir/gmapindex\" -d $dbname -F \"$dbdir\" -D \"$dbdir\" -L";
print STDERR "Running $cmd\n";
if (($rc = system($cmd)) != 0) {
die "$cmd failed with return code $rc";
@@ -386,7 +387,7 @@ sub make_enhanced_suffix_array {
sleep($sleeptime);
# Compressed suffix array
- # $cmd = "$bindir/gmapindex -d $dbname -F \"$dbdir\" -D \"$dbdir\" -C";
+ # $cmd = "\"$bindir/gmapindex\" -d $dbname -F \"$dbdir\" -D \"$dbdir\" -C";
# print STDERR "Running $cmd\n";
# if (($rc = system($cmd)) != 0) {
# die "$cmd failed with return code $rc";
--
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