feat: output the HN tag and optionally add the MD to the XA tag

build.py

@@ -1,12 +1,45 @@
 import multiprocessing
+import os
 import platform
+import subprocess
+from contextlib import contextmanager
 from pathlib import Path
 from typing import List
 
 from Cython.Build import cythonize
 from Cython.Distutils.build_ext import new_build_ext as cython_build_ext
 from setuptools import Extension, Distribution
 
+@contextmanager
+def changedir(path):
+    save_dir = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(save_dir)
+
+@contextmanager
+def with_patches():
+    patches = sorted([
+        os.path.abspath(patch)
+        for patch in Path("patches").iterdir()
+        if patch.is_file() and patch.suffix == ".patch"
+    ])
+    with changedir("bwa"):
+        for patch in patches:
+            retcode = subprocess.call(f"git apply {patch}", shell=True)
+            if retcode != 0:
+                raise RuntimeError(f"Failed to apply patch {patch}")
+    try:
+        yield
+    finally:
+        commands = ["git submodule deinit -f .", "git submodule update --init"]
+        for command in commands:
+            retcode = subprocess.call(command, shell=True)
+            if retcode != 0:
+                raise RuntimeError(f"Failed to reset submodules: {command}")
+
 SOURCE_DIR = Path("pybwa")
 BUILD_DIR = Path("cython_build")
 compile_args = []
@@ -110,46 +143,48 @@ def cythonize_helper(extension_modules: List[Extension]) -> List[Extension]:
 
 
 def build():
-    # Collect and cythonize all files
-    extension_modules = cythonize_helper([
-        libbwaindex_module,
-        libbwaaln_module,
-        libbwamem_module
-    ])
-
-    # Use Setuptools to collect files
-    distribution = Distribution({
-        "name": "pybwa",
-        'version': '0.0.1',
-        'description': 'Python bindings for BWA',
-        'long_description': __doc__,
-        'long_description_content_type': 'text/x-rst',
-        'author': 'Nils Homer',
-        'author_email': '[email protected]',
-        'license': 'MIT',
-        'platforms': ['POSIX', 'UNIX', 'MacOS'],
-        'classifiers': [_f for _f in CLASSIFIERS.split('\n') if _f],
-        'url': 'https://github.com/fulcrumgenomics/pybwa',
-        'packages': ['pybwa', 'pybwa.include.bwa'],
-        'package_dir': {'pybwa': 'pybwa', 'pybwa.include.bwa': 'bwa'},
-        'package_data': {'': ['*.pxd', '*.h', '*.c', 'py.typed', '*.pyi'], },
-        "ext_modules": extension_modules,
-        "cmdclass": {
-            "build_ext": cython_build_ext,
-        },
-    })
-
-    # Grab the build_ext command and copy all files back to source dir.
-    # Done so Poetry grabs the files during the next step in its build.
-    build_ext_cmd = distribution.get_command_obj("build_ext")
-    build_ext_cmd.ensure_finalized()
-    # Set the value to 1 for "inplace", with the goal to build extensions
-    # in build directory, and then copy all files back to the source dir
-    # (under the hood, "copy_extensions_to_source" will be called after
-    # building the extensions). This is done so Poetry grabs the files
-    # during the next step in its build.
-    build_ext_cmd.inplace = 1
-    build_ext_cmd.run()
+    # apply patches to bwa, then revert them after
+    with with_patches():
+        # Collect and cythonize all files
+        extension_modules = cythonize_helper([
+            libbwaindex_module,
+            libbwaaln_module,
+            libbwamem_module
+        ])
+
+        # Use Setuptools to collect files
+        distribution = Distribution({
+            "name": "pybwa",
+            'version': '0.0.1',
+            'description': 'Python bindings for BWA',
+            'long_description': __doc__,
+            'long_description_content_type': 'text/x-rst',
+            'author': 'Nils Homer',
+            'author_email': '[email protected]',
+            'license': 'MIT',
+            'platforms': ['POSIX', 'UNIX', 'MacOS'],
+            'classifiers': [_f for _f in CLASSIFIERS.split('\n') if _f],
+            'url': 'https://github.com/fulcrumgenomics/pybwa',
+            'packages': ['pybwa', 'pybwa.include.bwa'],
+            'package_dir': {'pybwa': 'pybwa', 'pybwa.include.bwa': 'bwa'},
+            'package_data': {'': ['*.pxd', '*.h', '*.c', 'py.typed', '*.pyi'], },
+            "ext_modules": extension_modules,
+            "cmdclass": {
+                "build_ext": cython_build_ext,
+            },
+        })
+
+        # Grab the build_ext command and copy all files back to source dir.
+        # Done so Poetry grabs the files during the next step in its build.
+        build_ext_cmd = distribution.get_command_obj("build_ext")
+        build_ext_cmd.ensure_finalized()
+        # Set the value to 1 for "inplace", with the goal to build extensions
+        # in build directory, and then copy all files back to the source dir
+        # (under the hood, "copy_extensions_to_source" will be called after
+        # building the extensions). This is done so Poetry grabs the files
+        # during the next step in its build.
+        build_ext_cmd.inplace = 1
+        build_ext_cmd.run()
 
 
 if __name__ == "__main__":

docs/api.rst

@@ -99,6 +99,14 @@ As a result, the mapping quality may also differ slightly.
 This is due to an implementation detail in which the order of random numbers used is different between this wrapper
 and command-line.
 
+Finally, the following additions have been made to :code:`bwa aln/samse`:
+
+#. The standard SAM tag :code:`HN` is added.  This is useful if we find too many hits
+   (:attr:`~pybwa.BwaAlnOptions.max_hits`) and therefore no hits are reported in the :code:`XA` tag, we can still
+   know how many were found.
+#. The :py:attr:`~pybwa.BwaAlnOptions.with_md` option will add the standard SAM tag :code:`MD` to the :code:`XA` tag, 
+   otherwise :code:`.` will be used.  This provides additional information on the quality of alternative alignments.
+
 ===
 API
 ===

patches/0001-feat-add-HN-tag-to-bwa-aln.patch

@@ -0,0 +1,76 @@
+From 7d36ae830fc7391cfa69ffcdf239755f01317c1c Mon Sep 17 00:00:00 2001
+From: Nils Homer <[email protected]>
+Date: Thu, 16 Jan 2025 22:35:13 -0800
+Subject: [PATCH 1/2] feat: add HN tag to bwa aln
+
+---
+ bwase.c  | 17 +++++++++--------
+ bwtaln.h |  1 +
+ 2 files changed, 10 insertions(+), 8 deletions(-)
+
+diff --git a/bwase.c b/bwase.c
+index 18e8671..eb43c02 100644
+--- a/bwase.c
++++ b/bwase.c
+@@ -21,7 +21,7 @@ int g_log_n[256];
+
+ void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
+ {
+-	int i, cnt, best;
++	int i, k, cnt, best;
+ 	if (n_aln == 0) {
+ 		s->type = BWA_TYPE_NO_MATCH;
+ 		s->c1 = s->c2 = 0;
+@@ -47,14 +47,14 @@ void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_ma
+ 		s->type = s->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
+ 	}
+
++	for (k = s->n_occ = 0; k < n_aln; ++k) {
++		const bwt_aln1_t *q = aln + k;
++		s->n_occ += q->l - q->k + 1;
++	}
+ 	if (n_multi) {
+-		int k, rest, n_occ, z = 0;
+-		for (k = n_occ = 0; k < n_aln; ++k) {
+-			const bwt_aln1_t *q = aln + k;
+-			n_occ += q->l - q->k + 1;
+-		}
++		int rest, z = 0;
+ 		if (s->multi) free(s->multi);
+-		if (n_occ > n_multi + 1) { // if there are too many hits, generate none of them
++		if (s->n_occ > n_multi + 1) { // if there are too many hits, generate none of them
+ 			s->multi = 0; s->n_multi = 0;
+ 			return;
+ 		}
+@@ -62,7 +62,7 @@ void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_ma
+ 		 * here. In principle, due to the requirement above, we can
+ 		 * simply output all hits, but the following samples "rest"
+ 		 * number of random hits. */
+-		rest = n_occ > n_multi + 1? n_multi + 1 : n_occ; // find one additional for ->sa
++		rest = s->n_occ > n_multi + 1? n_multi + 1 : s->n_occ; // find one additional for ->sa
+ 		s->multi = calloc(rest, sizeof(bwt_multi1_t));
+ 		for (k = 0; k < n_aln; ++k) {
+ 			const bwt_aln1_t *q = aln + k;
+@@ -477,6 +477,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
+ 				}
+ 			}
+ 		}
++		err_printf("\tHN:i:%d", p->n_occ);
+ 		err_putchar('\n');
+ 	} else { // this read has no match
+ 		//ubyte_t *s = p->strand? p->rseq : p->seq;
+diff --git a/bwtaln.h b/bwtaln.h
+index 4616ff5..71ea627 100644
+--- a/bwtaln.h
++++ b/bwtaln.h
+@@ -76,6 +76,7 @@ typedef struct {
+ 	// multiple hits
+ 	int n_multi;
+ 	bwt_multi1_t *multi;
++	int n_occ; // total # of hits found, not just those reported in XA, output in HN
+ 	// alignment information
+ 	bwtint_t sa, pos;
+ 	uint64_t c1:28, c2:28, seQ:8; // number of top1 and top2 hits; single-end mapQ
+-- 
+2.39.5 (Apple Git-154)
+