minibwa 0.0.0

data/ext/minibwa/mb_options.c

@@ -0,0 +1,301 @@
+/*
+ * Minibwa::Options -- wraps mb_opt_t, the alignment parameter block.
+ *
+ * The struct is stored by value inside a TypedData object, so copying an
+ * Options never aliases C memory. Every one of its ~50 fields is exposed as
+ * a reader/writer pair generated from an X-macro table, keeping the accessor
+ * list to one line per field as upstream adds them. Also wraps mb_opt_init()
+ * and mb_opt_preset() ("sr", "adap", "lr") and turns each MB_F_* bit into a
+ * predicate/setter pair.
+ */
+
+#include "minibwa.h"
+
+const rb_data_type_t rb_minibwa_options_type = {
+    .wrap_struct_name = "Minibwa::Options",
+    .function = { NULL, RUBY_DEFAULT_FREE, NULL },
+    .flags = RUBY_TYPED_FREE_IMMEDIATELY
+};
+
+/* ------------------------------------------------------------------ */
+/* X-macro: field name, C type, Ruby wrap/unwrap macros               */
+/* ------------------------------------------------------------------ */
+
+#define INT32_FIELD(name)   FIELD(name, int32_t,  NUM2INT,  INT2NUM)
+#define INT64_FIELD(name)   FIELD(name, int64_t,  NUM2LL,  LL2NUM)
+#define UINT64_FIELD(name)  FIELD(name, uint64_t, NUM2ULL, ULL2NUM)
+#define FLOAT_FIELD(name)   FIELD(name, float,    NUM2DBL, DBL2NUM)
+
+#define FIELD(name, ctype, unwrap, wrap)                              \
+    static VALUE                                                      \
+    mb_opt_get_##name(VALUE self)                                     \
+    {                                                                 \
+        mb_opt_t *opt = rb_minibwa_get_opt(self);                     \
+        return wrap(opt->name);                                       \
+    }                                                                 \
+    static VALUE                                                      \
+    mb_opt_set_##name(VALUE self, VALUE val)                          \
+    {                                                                 \
+        mb_opt_t *opt = rb_minibwa_get_opt(self);                     \
+        opt->name = (ctype)unwrap(val);                               \
+        return val;                                                   \
+    }
+
+/* ---- flag (uint64_t, special: also has bit predicates/setters) ---- */
+UINT64_FIELD(flag)
+
+/* ---- seeding options ---- */
+INT32_FIELD(min_len)
+INT32_FIELD(max_sub_occ)
+INT32_FIELD(max_occ)
+
+/* ---- general algorithm options ---- */
+INT32_FIELD(bw)
+INT32_FIELD(bw_long)
+INT32_FIELD(max_gap)
+INT32_FIELD(max_sr_len)
+
+/* ---- chaining options ---- */
+INT32_FIELD(max_chain_skip)
+INT32_FIELD(max_chain_iter)
+INT32_FIELD(min_chain_score)
+FLOAT_FIELD(chain_gap_scale)
+
+/* ---- hit processing options ---- */
+FLOAT_FIELD(mask_level)
+INT32_FIELD(mask_len)
+FLOAT_FIELD(pri_ratio)
+INT32_FIELD(best_n)
+
+/* ---- alignment options ---- */
+INT32_FIELD(a)
+INT32_FIELD(b)
+INT32_FIELD(b_ts)
+INT32_FIELD(b_ambi)
+INT32_FIELD(q)
+INT32_FIELD(q2)
+INT32_FIELD(e)
+INT32_FIELD(e2)
+INT32_FIELD(end_bonus)
+INT32_FIELD(min_dp_max)
+INT32_FIELD(zdrop)
+INT32_FIELD(zdrop_inv)
+INT32_FIELD(min_ksw_len)
+
+/* ---- pairing options ---- */
+INT32_FIELD(max_pe_ins)
+INT32_FIELD(max_rescue)
+INT32_FIELD(pen_unpair)
+INT32_FIELD(pe_avg)
+INT32_FIELD(pe_std)
+INT32_FIELD(pe_lo)
+INT32_FIELD(pe_hi)
+
+/* ---- input/output options ---- */
+INT32_FIELD(sb_len)
+INT32_FIELD(sb_seq)
+INT32_FIELD(n_thread)
+INT32_FIELD(out_n)
+FLOAT_FIELD(out_s)
+INT32_FIELD(seed)
+INT32_FIELD(xa_max)
+INT64_FIELD(mb_size)
+INT64_FIELD(max_mb_size)
+INT64_FIELD(max_sw_mat)
+INT64_FIELD(cap_kalloc)
+
+#undef FIELD
+#undef INT32_FIELD
+#undef INT64_FIELD
+#undef UINT64_FIELD
+#undef FLOAT_FIELD
+
+/* ------------------------------------------------------------------ */
+/* Flag bit predicates and setters                                    */
+/* ------------------------------------------------------------------ */
+
+#define FLAG_BIT(name, bit)                                            \
+    static VALUE                                                      \
+    mb_opt_##name##_p(VALUE self)                                     \
+    {                                                                 \
+        mb_opt_t *opt = rb_minibwa_get_opt(self);                     \
+        return (opt->flag & bit) ? Qtrue : Qfalse;                    \
+    }                                                                 \
+    static VALUE                                                      \
+    mb_opt_set_##name(VALUE self, VALUE val)                          \
+    {                                                                 \
+        mb_opt_t *opt = rb_minibwa_get_opt(self);                     \
+        if (RTEST(val)) opt->flag |= bit;                             \
+        else           opt->flag &= ~bit;                              \
+        return val;                                                   \
+    }
+
+FLAG_BIT(paf,           MB_F_PAF)
+FLAG_BIT(no_unmap,      MB_F_NO_UNMAP)
+FLAG_BIT(copy_comment,  MB_F_COPY_COMMENT)
+FLAG_BIT(pe,            MB_F_PE)
+FLAG_BIT(long_mode,     MB_F_LONG)
+FLAG_BIT(eqx,           MB_F_EQX)
+FLAG_BIT(no_kalloc,     MB_F_NO_KALLOC)
+FLAG_BIT(no_aln,        MB_F_NO_ALN)
+FLAG_BIT(pe_predef,     MB_F_PE_PREDEF)
+FLAG_BIT(write_ds,      MB_F_WRITE_DS)
+FLAG_BIT(write_cs,      MB_F_WRITE_CS)
+FLAG_BIT(write_md,      MB_F_WRITE_MD)
+FLAG_BIT(second_seq,    MB_F_2ND_SEQ)
+FLAG_BIT(supp_soft,     MB_F_SUPP_SOFT)
+FLAG_BIT(adap,          MB_F_ADAP)
+FLAG_BIT(primary5,      MB_F_PRIMARY5)
+FLAG_BIT(no_pairing,    MB_F_NO_PAIRING)
+FLAG_BIT(meth,          MB_F_METH)
+
+#undef FLAG_BIT
+
+/* ------------------------------------------------------------------ */
+/* Constructor, init, preset                                          */
+/* ------------------------------------------------------------------ */
+
+static VALUE
+mb_opt_alloc(VALUE klass)
+{
+    mb_opt_t *opt;
+    VALUE obj = TypedData_Make_Struct(klass, mb_opt_t,
+                                      &rb_minibwa_options_type, opt);
+    mb_opt_init(opt);
+    return obj;
+}
+
+/*
+ * call-seq:
+ *   Options.new(**kwargs) -> Options
+ *
+ * Returns a new Options initialised with mb_opt_init() (adaptive paired-end
+ * defaults).  Pass keyword arguments to override individual fields, e.g.
+ *
+ *   Options.new(bw: 500, min_len: 19)
+ */
+static VALUE
+mb_opt_initialize(int argc, VALUE *argv, VALUE self)
+{
+    VALUE kwargs;
+    rb_scan_args(argc, argv, ":", &kwargs);
+
+    if (!NIL_P(kwargs)) {
+        static ID id_keyword_new;
+        if (!id_keyword_new)
+            id_keyword_new = rb_intern("__keyword_new__");
+        /* Delegate to Ruby-side keyword handling in lib/minibwa/options.rb */
+        rb_funcall(self, id_keyword_new, 1, kwargs);
+    }
+    return Qnil;
+}
+
+/*
+ * call-seq:
+ *   preset!(name) -> true or false
+ *
+ * Applies a named preset.  Returns +true+ on success, +false+ if the preset
+ * name is unknown.  Known presets: "sr", "adap", "lr".
+ */
+static VALUE
+rb_minibwa_opt_preset(VALUE self, VALUE name)
+{
+    mb_opt_t *opt = rb_minibwa_get_opt(self);
+    const char *s = StringValueCStr(name);
+    return mb_opt_preset(opt, s) == 0 ? Qtrue : Qfalse;
+}
+
+/* ------------------------------------------------------------------ */
+/* Registration                                                       */
+/* ------------------------------------------------------------------ */
+
+#define DEF_ACCESSOR(klass, name)                                      \
+    rb_define_method(klass, #name, mb_opt_get_##name, 0);             \
+    rb_define_method(klass, #name "=", mb_opt_set_##name, 1);
+
+#define DEF_FLAG(klass, name)                                          \
+    rb_define_method(klass, #name "?", mb_opt_##name##_p, 0);         \
+    rb_define_method(klass, #name "=", mb_opt_set_##name, 1);
+
+void
+rb_minibwa_init_options(void)
+{
+    VALUE klass = rb_define_class_under(rb_mMinibwa, "Options", rb_cObject);
+    rb_cMinibwaOptions = klass;
+
+    rb_define_alloc_func(klass, mb_opt_alloc);
+    rb_define_method(klass, "initialize", mb_opt_initialize, -1);
+    rb_define_method(klass, "preset!", rb_minibwa_opt_preset, 1);
+
+    /* ---- scalar fields ---- */
+    DEF_ACCESSOR(klass, flag)
+    DEF_ACCESSOR(klass, min_len)
+    DEF_ACCESSOR(klass, max_sub_occ)
+    DEF_ACCESSOR(klass, max_occ)
+    DEF_ACCESSOR(klass, bw)
+    DEF_ACCESSOR(klass, bw_long)
+    DEF_ACCESSOR(klass, max_gap)
+    DEF_ACCESSOR(klass, max_sr_len)
+    DEF_ACCESSOR(klass, max_chain_skip)
+    DEF_ACCESSOR(klass, max_chain_iter)
+    DEF_ACCESSOR(klass, min_chain_score)
+    DEF_ACCESSOR(klass, chain_gap_scale)
+    DEF_ACCESSOR(klass, mask_level)
+    DEF_ACCESSOR(klass, mask_len)
+    DEF_ACCESSOR(klass, pri_ratio)
+    DEF_ACCESSOR(klass, best_n)
+    DEF_ACCESSOR(klass, a)
+    DEF_ACCESSOR(klass, b)
+    DEF_ACCESSOR(klass, b_ts)
+    DEF_ACCESSOR(klass, b_ambi)
+    DEF_ACCESSOR(klass, q)
+    DEF_ACCESSOR(klass, q2)
+    DEF_ACCESSOR(klass, e)
+    DEF_ACCESSOR(klass, e2)
+    DEF_ACCESSOR(klass, end_bonus)
+    DEF_ACCESSOR(klass, min_dp_max)
+    DEF_ACCESSOR(klass, zdrop)
+    DEF_ACCESSOR(klass, zdrop_inv)
+    DEF_ACCESSOR(klass, min_ksw_len)
+    DEF_ACCESSOR(klass, max_pe_ins)
+    DEF_ACCESSOR(klass, max_rescue)
+    DEF_ACCESSOR(klass, pen_unpair)
+    DEF_ACCESSOR(klass, pe_avg)
+    DEF_ACCESSOR(klass, pe_std)
+    DEF_ACCESSOR(klass, pe_lo)
+    DEF_ACCESSOR(klass, pe_hi)
+    DEF_ACCESSOR(klass, sb_len)
+    DEF_ACCESSOR(klass, sb_seq)
+    DEF_ACCESSOR(klass, n_thread)
+    DEF_ACCESSOR(klass, out_n)
+    DEF_ACCESSOR(klass, out_s)
+    DEF_ACCESSOR(klass, seed)
+    DEF_ACCESSOR(klass, xa_max)
+    DEF_ACCESSOR(klass, mb_size)
+    DEF_ACCESSOR(klass, max_mb_size)
+    DEF_ACCESSOR(klass, max_sw_mat)
+    DEF_ACCESSOR(klass, cap_kalloc)
+
+    /* ---- flag bits ---- */
+    DEF_FLAG(klass, paf)
+    DEF_FLAG(klass, no_unmap)
+    DEF_FLAG(klass, copy_comment)
+    DEF_FLAG(klass, pe)
+    DEF_FLAG(klass, long_mode)
+    DEF_FLAG(klass, eqx)
+    DEF_FLAG(klass, no_kalloc)
+    DEF_FLAG(klass, no_aln)
+    DEF_FLAG(klass, pe_predef)
+    DEF_FLAG(klass, write_ds)
+    DEF_FLAG(klass, write_cs)
+    DEF_FLAG(klass, write_md)
+    DEF_FLAG(klass, second_seq)
+    DEF_FLAG(klass, supp_soft)
+    DEF_FLAG(klass, adap)
+    DEF_FLAG(klass, primary5)
+    DEF_FLAG(klass, no_pairing)
+    DEF_FLAG(klass, meth)
+}
+
+#undef DEF_ACCESSOR
+#undef DEF_FLAG

data/ext/minibwa/minibwa/LICENSE.txt

@@ -0,0 +1,37 @@
+The MIT License
+
+Copyright (c) 2025-     Dana-Farber Cancer Institute
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+---
+
+THIRD-PARTY SOFTWARE NOTICES
+
+This project includes the source code from the following projects:
+
+ * libsais: Apache 2 License. Copyright (c) 2021-2025 Ilya Grebnov <ilya.grebnov@gmail.com>
+ * mimalloc: MIT License. Copyright (c) 2018-2026 Microsoft Corporation, Daan Leijen
+
+It is optionally built on the following projects (disabled with "make gpl=0"):
+
+ * QSufSort: HPND License. Copyright (c) 1999 N. Jesper Larsson
+ * bwtgen: GPL 2 License. Copyright (c) 2004 Wong Chi Kwong