reinstate warning for index file older than FASTA

brentp · Nov 28, 2022 · cddbadf · cddbadf
1 parent acfc394
commit cddbadf
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Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/src/utils/Fasta/Fasta.cpp b/src/utils/Fasta/Fasta.cpp
@@ -35,11 +35,21 @@ FastaIndex::FastaIndex(bool useFullHeader)
 void FastaIndex::readIndexFile(string fname) {
 
     faidx = fai_load(fname.c_str());
+    const char *idx_path = (fname + ".fai").c_str();
+
     // NOTE: can use faidx_set_cache_size to improve performance of repeated queries.
     if(faidx == NULL) {
         cerr << "Warning: malformed fasta index file " << fname <<  endl;
         exit(1);
     }
+
+    struct stat index_attr, fasta_attr;
+    stat(idx_path, &index_attr);
+    stat(fname.c_str(), &fasta_attr);
+    if(fasta_attr.st_mtime > index_attr.st_mtime) {
+        cerr << "Warning: the index file is older than the FASTA file." << endl;
+    }
+
     int n_seq = faidx_nseq(faidx);
     for(int i = 0; i < n_seq; i++){
         const char* chrom_name = faidx_iseq(faidx, i);

diff --git a/src/utils/Fasta/Fasta.h b/src/utils/Fasta/Fasta.h
@@ -48,7 +48,6 @@ class FastaIndex : public map<string, FastaIndexEntry> {
         vector<string> sequenceNames;
         void indexReference(string refName);
         void readIndexFile(string fname);
-        //void writeIndexFile(string fname);
         FastaIndexEntry entry(string key);
         bool chromFound(string name);
         void flushEntryToIndex(FastaIndexEntry& entry);
@@ -64,8 +63,6 @@ class FastaReference {
         bool usingfullheader;
         FastaReference(void) : usingmmap(false), usingfullheader(false) { }
         ~FastaReference(void);
-        //FILE* file;
-        //void* filemm;
         size_t filesize;
         FastaIndex* index;
         vector<FastaIndexEntry> findSequencesStartingWith(string seqnameStart);

diff --git a/test/getfasta/test-getfasta.sh b/test/getfasta/test-getfasta.sh
@@ -113,7 +113,7 @@ check obs exp
 rm obs exp test.iupac.fa.fai
 
 # test the warning about an outdated FASTA index file
-echo -e "    getfasta.t10..disabled..\c"
+echo -e "    getfasta.t10...\c"
 echo \
 ">chr1
 cggggggggg
@@ -127,7 +127,7 @@ touch test.fa
 echo -e "chr2\t2\t10" | $BT getfasta -fi test.fa -bed -  \
 	> /dev/null 2> obs
 echo "Warning: the index file is older than the FASTA file." > exp
-#check obs exp
+check obs exp
 rm obs exp test.fa test.fa.fai