Merge pull request #242 from gtamazian/getfasta-fixes

Getfasta fixes

src/utils/Fasta/Fasta.cpp

@@ -244,7 +244,14 @@ void FastaReference::open(string reffilename, bool usemmap, bool useFullHeader)
     struct stat stFileInfo; 
     string indexFileName = filename + index->indexFileExtension(); 
     // if we can find an index file, use it
-    if(stat(indexFileName.c_str(), &stFileInfo) == 0) { 
+    if(stat(indexFileName.c_str(), &stFileInfo) == 0) {
+        // check if the index file is older than the FASTA file
+        struct stat index_attrib, fasta_attrib;
+        stat(indexFileName.c_str(), &index_attrib);
+        stat(reffilename.c_str(), &fasta_attrib);
+        if (fasta_attrib.st_mtime > index_attrib.st_mtime) {
+            cerr << "Warning: the index file is older than the FASTA file." << endl;
+        }
         index->readIndexFile(indexFileName);
     } else { // otherwise, read the reference and generate the index file in the cwd
         cerr << "index file " << indexFileName << " not found, generating..." << endl;

test/getfasta/test-getfasta.sh

@@ -88,7 +88,7 @@ AGCTYRWSKMDVHBXN
 agctyrwskmdvhbxn" > exp
 $BT getfasta  -fi test.iupac.fa -bed test.iupac.bed -fo - > obs
 check obs exp
-rm obs exp
+rm obs exp test.iupac.fa.fai
 
 
 # test IUPAC revcomp
@@ -100,4 +100,23 @@ NXVDBHKMSWYRAGCT
 nxvdbhkmswyragct" > exp
 $BT getfasta  -fi test.iupac.fa -bed test.iupac.bed -s -fo - > obs
 check obs exp
-rm obs exp
+rm obs exp test.iupac.fa.fai
+
+# test the warning about an outdated FASTA index file
+echo "    getfasta.t10...\c"
+echo \
+">chr1
+cggggggggg
+>chr2
+AAATTTTTTTTTT" > test.fa
+# create an index file
+echo -e "chr2\t2\t10" | $BT getfasta -fi test.fa -bed - -fo - > /dev/null
+# modify the FASTA file in a second
+sleep 1 
+touch test.fa
+echo -e "chr2\t2\t10" | $BT getfasta -fi test.fa -bed - -fo - \
+	> /dev/null 2> obs
+echo "Warning: the index file is older than the FASTA file." > exp
+check obs exp
+rm obs exp test.fa test.fa.fai
+

test/getfasta/test.iupac.bed

+1	0	16	1	1000	-
+2	0	16	1	1000	-

test/getfasta/test.iupac.fa

+>1
+AGCTYRWSKMDVHBXNACGT
+>2
+agctyrwskmdvhbxnacgt