Shakedown (#2)

* Correct some documentation
* Skip pointless allocations where there are no alignments
* Fix bug in subscripting of records when collating

README.md

@@ -23,7 +23,7 @@ makes some amendments to the bwa/Makefile. To build and install the package one
 therefore run:
 
     git clone --recursive https://git/research/bwapy.git
-    make libbwa.a 
+    make bwa/libbwa.a 
     python setup.py install
 
 
@@ -36,9 +36,12 @@ alignments of sequences given as strings:
 
 ```python
 from bwapy import BwaAligner
-aligner = BwaAligner(args.index)
+index = 'path/to/index' # the path given to bwa index
+seq = 'ACGATCGCGATCGA'
+
+aligner = BwaAligner(index)
 alignments = aligner.align_seq(seq)
-print('Found {} alignments for input {}.'.format(len(alignments), i))
+print('Found {} alignments.'.format(len(alignments))
 for aln in alignments:
     print('  ', aln)
 ```

bwapy/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '0.1.0'
+__version__ = '0.1.1'
 
 from bwapy.libbwa import BwaAligner

bwapy/libbwa.py

@@ -178,8 +178,11 @@ def align_seq(self, seq:str):
         :returns: tuple of :class:`Alignment`
         """
         alns = libbwa.align(self.index, seq.encode())
-        alignments = tuple(self._build_alignment(alns.aln[i]) for i in range(alns.n))
-        libbwa.free_mem_aln_v(alns)
+        if alns == ffi.NULL:
+            alignments = tuple()
+        else:
+            alignments = tuple(self._build_alignment(alns.aln[i]) for i in range(alns.n))
+            libbwa.free_mem_aln_v(alns)
         return alignments
 
 

bwapy/libbwapy.c

@@ -107,16 +107,24 @@ mem_aln_v *align(bwaidx_t * idx, char * seq) {
 		if (ar.a[i].secondary >= 0) continue;
 		primary++;
 	}
-	mem_aln_v *alns = new_mem_aln_v(primary);
-	alns->n = primary;
 
-        for (size_t i = 0; i < ar.n; ++i) {
-		if (ar.a[i].secondary >= 0) continue;
-		alns->aln[i] = mem_reg2aln(opt, idx->bns, idx->pac, seq_len, seq, &ar.a[i]);
-	}
+        if(primary == 0){
+		free(ar.a);
+		free(opt);
+		return NULL;
+	} else {
+		mem_aln_v *alns = new_mem_aln_v(primary);
+		alns->n = primary;
+
+		primary = 0;
+        	for (size_t i = 0; i < ar.n; ++i) {
+			if (ar.a[i].secondary >= 0) continue;
+			alns->aln[primary++] = mem_reg2aln(opt, idx->bns, idx->pac, seq_len, seq, &ar.a[i]);
+		}
 
-	free(ar.a);
-	free(opt);
+		free(ar.a);
+		free(opt);
 
-	return alns;
+		return alns;
+	}
 }

docs/index.rst

@@ -21,7 +21,7 @@ therefore run:
 .. code-block:: bash
 
     git clone --recursive https://git/research/bwapy.git
-    make libbwa.a 
+    make bwa/libbwa.a 
     python setup.py install
 
 
@@ -35,9 +35,12 @@ alignments of sequences given as strings:
 .. code-block:: python
 
     from bwapy import BwaAligner
-    aligner = BwaAligner(args.index)
+    index = 'path/to/index' # the path given to bwa index
+    seq = 'ACGATCGCGATCGA'
+
+    aligner = BwaAligner(index)
     alignments = aligner.align_seq(seq)
-    print('Found {} alignments for input {}.'.format(len(alignments), i))
+    print('Found {} alignments.'.format(len(alignments))
     for aln in alignments:
         print('  ', aln)