Fix mummerplot space issue. Fixes #206

* Don't require a space before an alignment information in the output
  of mummer. It is a FASTA format, headers are already marked by '>',
  data shouldn't require a space. Used to break when indices were
  larger than 8 digits long.

Author: gmarcais

.gitignore

@@ -14,3 +14,5 @@ missing
 autom4te.cache
 compile
 test-driver
+compile_commands.json
+.deps

scripts/mummerplot.pl

@@ -516,7 +516,7 @@ ($)
 
     while ( <MFILE> ) {
         #-- match
-        if ( /^\s+(\d+)\s+(\d+)\s+(\d+)\s+\S+\s+\S+$/ ) {
+        if ( /^\s*(\d+)\s+(\d+)\s+(\d+)\s+\S+\s+\S+$/ ) {
             @align = ($1, $1, $2, $2, 100, $lenR, $lenQ, $idR, $idQ);
             $len = $3 - 1;
             $align[1] += $dR == 1 ? $len : -$len;
@@ -563,7 +563,7 @@ ($)
 
     while ( <MFILE> ) {
         #-- 3 column match
-        if ( /^\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {
+        if ( /^\s*(\d+)\s+(\d+)\s+(\d+)$/ ) {
             @align = ($1, $1, $2, $2, 100, 0, $lenQ, "REF", $idQ);
             $len = $3 - 1;
             $align[1] += $len;
@@ -573,7 +573,7 @@ ($)
         }
 
         #-- 4 column match
-        if ( /^\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {
+        if ( /^\s*(\S+)\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {
             @align = ($2, $2, $3, $3, 100, 0, $lenQ, $1, $idQ);
             $len = $4 - 1;
             $align[1] += $len;

tests/Makefile.am

@@ -72,7 +72,7 @@ TEST_EXTENSIONS += .sh
 SH_LOG_COMPILER = %D%/testsh
 
 # List of tests to run
-script_tests = %D%/save_load.sh %D%/batch.sh %D%/mummer.sh %D%/nucmer.sh %D%/sam.sh %D%/genome.sh %D%/delta-filter.sh
+script_tests = %D%/save_load.sh %D%/batch.sh %D%/mummer.sh %D%/nucmer.sh %D%/sam.sh %D%/genome.sh %D%/delta-filter.sh %D%/mummerplot.sh
 EXTRA_DIST += $(script_tests)
 TESTS += $(script_tests)
 

tests/mummerplot.sh

@@ -0,0 +1,8 @@
+mummer -mum -b -c -n $D/small_genome.fa $D/small_reads_0.fa > small_0.mums
+
+mummerplot -t png -p with_spaces small_0.mums
+sed 's/^ \+//' < small_0.mums > small_0_nospace.mums
+mummerplot -t png -p no_space small_0_nospace.mums
+
+diff with_spaces.fplot no_space.fplot
+diff with_spaces.rplot no_space.rplot