Fix bam indexing for large chromosomes

Large genomes with large chromosomes (larger than some 500Mb) cannot be indexed by samtools index in "bai" format.  The requirement is to use the "csi" index instead.  The changes in this commit introduce "csi" when the "bai" fails

Author: maol-corteva

src/read_mapper.py

@@ -378,6 +378,18 @@ def align_fasta(aligner, fastq_file, annotation_file, args, label, out_dir):
     logger.info("Indexing alignments")
     try:
         pysam.index(alignment_bam_path)
+    except pysam.SamtoolsError as err:
+        if "failed to create index" in err.value:
+            logger.info(f"Samtools failed to generate default .bai index; with error: {err.value}")
+            logger.info("Trying to build a CSI index instead")
+            try:
+                pysam.index('-@', str(args.threads), '-c', alignment_bam_path)
+            except pysam.SamtoolsError as err:
+                logger.error(f"Failed to create CSI index: {err.value}")
+                exit(-1)
+        else:
+            logger.error(err.value)
+            exit(-1) 
     except OSError as err:
         logger.error(err)
         exit(-1)