--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bamtk.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,119 @@
+#include <stdio.h>
+#include <unistd.h>
+#include <assert.h>
+#include <fcntl.h>
+#include "bam.h"
+
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+int bam_taf2baf(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
+int bam_merge(int argc, char *argv[]);
+int bam_index(int argc, char *argv[]);
+int bam_sort(int argc, char *argv[]);
+int bam_tview_main(int argc, char *argv[]);
+int bam_mating(int argc, char *argv[]);
+int bam_rmdup(int argc, char *argv[]);
+int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
+int bam_idxstats(int argc, char *argv[]);
+int main_samview(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_cut_target(int argc, char *argv[]);
+int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
+int main_depth(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
+int main_pad2unpad(int argc, char *argv[]);
+int main_bedcov(int argc, char *argv[]);
+int main_bamshuf(int argc, char *argv[]);
+
+int faidx_main(int argc, char *argv[]);
+
+static int usage()
+{
+	fprintf(stderr, "\n");
+	fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
+	fprintf(stderr, "Version: %s\n\n", BAM_VERSION);
+	fprintf(stderr, "Usage:   samtools <command> [options]\n\n");
+	fprintf(stderr, "Command: view        SAM<->BAM conversion\n");
+	fprintf(stderr, "         sort        sort alignment file\n");
+	fprintf(stderr, "         mpileup     multi-way pileup\n");
+	fprintf(stderr, "         depth       compute the depth\n");
+	fprintf(stderr, "         faidx       index/extract FASTA\n");
+#if _CURSES_LIB != 0
+	fprintf(stderr, "         tview       text alignment viewer\n");
+#endif
+	fprintf(stderr, "         index       index alignment\n");
+	fprintf(stderr, "         idxstats    BAM index stats (r595 or later)\n");
+	fprintf(stderr, "         fixmate     fix mate information\n");
+	fprintf(stderr, "         flagstat    simple stats\n");
+	fprintf(stderr, "         calmd       recalculate MD/NM tags and '=' bases\n");
+	fprintf(stderr, "         merge       merge sorted alignments\n");
+	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
+	fprintf(stderr, "         reheader    replace BAM header\n");
+	fprintf(stderr, "         cat         concatenate BAMs\n");
+	fprintf(stderr, "         bedcov      read depth per BED region\n");
+	fprintf(stderr, "         targetcut   cut fosmid regions (for fosmid pool only)\n");
+	fprintf(stderr, "         phase       phase heterozygotes\n");
+	fprintf(stderr, "         bamshuf     shuffle and group alignments by name\n");
+//	fprintf(stderr, "         depad       convert padded BAM to unpadded BAM\n"); // not stable
+	fprintf(stderr, "\n");
+#ifdef _WIN32
+	fprintf(stderr, "\
+Note: The Windows version of SAMtools is mainly designed for read-only\n\
+      operations, such as viewing the alignments and generating the pileup.\n\
+      Binary files generated by the Windows version may be buggy.\n\n");
+#endif
+	return 1;
+}
+
+int main(int argc, char *argv[])
+{
+#ifdef _WIN32
+	setmode(fileno(stdout), O_BINARY);
+	setmode(fileno(stdin),  O_BINARY);
+#ifdef _USE_KNETFILE
+	knet_win32_init();
+#endif
+#endif
+	if (argc < 2) return usage();
+	if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
+	else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
+	else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
+	else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
+	else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
+	else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
+	else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
+	else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
+	else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
+	else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
+	else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
+	else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
+	else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
+	else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
+	else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
+	else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
+	else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
+	else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
+	else if (strcmp(argv[1], "pad2unpad") == 0) return main_pad2unpad(argc-1, argv+1);
+	else if (strcmp(argv[1], "depad") == 0) return main_pad2unpad(argc-1, argv+1);
+	else if (strcmp(argv[1], "bedcov") == 0) return main_bedcov(argc-1, argv+1);
+	else if (strcmp(argv[1], "bamshuf") == 0) return main_bamshuf(argc-1, argv+1);
+	else if (strcmp(argv[1], "pileup") == 0) {
+		fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
+		return 1;
+	}
+#if _CURSES_LIB != 0
+	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
+#endif
+	else {
+		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+		return 1;
+	}
+	return 0;	
+}