replace samtools headers with samtools_compat.h

Author: amkram

src/pileup.h

@@ -1,12 +1,4 @@
-#include <htslib/cram.h>
-#include <htslib/faidx.h>
-#include <htslib/hts.h>
-#include <htslib/khash_str2int.h>
-#include <htslib/klist.h>
-#include <htslib/kstring.h>
-#include <htslib/sam.h>
-#include <samtools/bam_plcmd.h>
-#include <samtools/samtools.h>
+#include "samtools_compat.h"
 
 void bam_and_ref_to_mplp(sam_hdr_t *header, bam1_t **bam_lines, int nbams,
                          char *ref_string, int lref, kstring_t *mplp_string);

src/samtools_compat.h

@@ -0,0 +1,126 @@
+/*
+ * samtools_compat.h -- Minimal struct definitions extracted from samtools
+ * for panmap's pileup module. Avoids linking against libst.a.
+ *
+ * Original sources: samtools/bam_plcmd.h, samtools/sam_opts.h
+ * Copyright (C) 2008-2024 Genome Research Ltd.
+ * License: MIT/Expat (same as samtools)
+ */
+
+#ifndef SAMTOOLS_COMPAT_H
+#define SAMTOOLS_COMPAT_H
+
+#include <stdio.h>
+#include <string.h>
+#include <stdarg.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include <htslib/kstring.h>
+#include <htslib/klist.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/cram.h>
+
+/* --- From sam_opts.h --- */
+
+typedef struct sam_global_args {
+    htsFormat in;
+    htsFormat out;
+    char *reference;
+    int nthreads;
+    int write_index;
+} sam_global_args;
+
+static inline void sam_global_args_init(sam_global_args *ga) {
+    if (ga) memset(ga, 0, sizeof(*ga));
+}
+
+/* --- From bam_plcmd.h --- */
+
+#define MPLP_NO_COMP    (1<<2)
+#define MPLP_NO_ORPHAN  (1<<3)
+#define MPLP_REALN      (1<<4)
+#define MPLP_NO_INDEL   (1<<5)
+#define MPLP_REDO_BAQ   (1<<6)
+#define MPLP_ILLUMINA13 (1<<7)
+#define MPLP_IGNORE_RG  (1<<8)
+#define MPLP_SMART_OVERLAPS (1<<10)
+
+#define MPLP_PRINT_MAPQ_CHAR (1<<11)
+#define MPLP_PRINT_QPOS  (1<<12)
+#define MPLP_PRINT_QNAME (1<<13)
+#define MPLP_PRINT_FLAG  (1<<14)
+#define MPLP_PRINT_RNAME (1<<15)
+#define MPLP_PRINT_POS   (1<<16)
+#define MPLP_PRINT_MAPQ  (1<<17)
+#define MPLP_PRINT_CIGAR (1<<18)
+#define MPLP_PRINT_RNEXT (1<<19)
+#define MPLP_PRINT_PNEXT (1<<20)
+#define MPLP_PRINT_TLEN  (1<<21)
+#define MPLP_PRINT_SEQ   (1<<22)
+#define MPLP_PRINT_QUAL  (1<<23)
+#define MPLP_PRINT_RLEN  (1<<24)
+#define MPLP_PRINT_MODS  (1<<25)
+#define MPLP_PRINT_QPOS5 (1<<26)
+#define MPLP_PRINT_LAST  (1<<27)
+
+#define MPLP_MAX_DEPTH 8000
+#define MPLP_MAX_INDEL_DEPTH 250
+
+typedef struct {
+    int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, all, rev_del;
+    int rflag_require, rflag_filter;
+    char *reg, *pl_list, *fai_fname, *output_fname;
+    faidx_t *fai;
+    void *bed, *rghash, *auxlist;
+    int argc;
+    char **argv;
+    char sep, empty, no_ins, no_ins_mods, no_del, no_ends;
+    sam_global_args ga;
+} mplp_conf_t;
+
+typedef struct {
+    char *ref[2];
+    int ref_id[2];
+    hts_pos_t ref_len[2];
+} mplp_ref_t;
+
+#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
+
+typedef struct {
+    samFile *fp;
+    hts_itr_t *iter;
+    sam_hdr_t *h;
+    mplp_ref_t *ref;
+    const mplp_conf_t *conf;
+} mplp_aux_t;
+
+typedef struct {
+    int n;
+    int *n_plp, *m_plp;
+    bam_pileup1_t **plp;
+} mplp_pileup_t;
+
+/* --- Inline replacements for samtools utility functions --- */
+
+static inline void print_error(const char *subcommand, const char *fmt, ...) {
+    va_list args;
+    fprintf(stderr, "[%s] ", subcommand);
+    va_start(args, fmt);
+    vfprintf(stderr, fmt, args);
+    va_end(args);
+    fprintf(stderr, "\n");
+}
+
+/*
+ * bed_overlap is called in pileup.c but only when conf->bed != NULL.
+ * panmap never sets conf->bed, so these calls are dead code.
+ * Provide a stub that always returns 0 to satisfy the linker.
+ */
+static inline int bed_overlap(const void *bed, const char *seq,
+                              hts_pos_t start, hts_pos_t end) {
+    (void)bed; (void)seq; (void)start; (void)end;
+    return 0;
+}
+
+#endif /* SAMTOOLS_COMPAT_H */