X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=9df7c118ef595ba48f1b6760aafad84300ed18dd;hb=ccb7838cb53bf0ca6917a77f7991d940057c12db;hp=0941f6f16f9194db93b152a48e2007b63f498d54;hpb=ea89c550a4ca078a462dc66dfcf77e65b09e1f2f;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index 0941f6f..9df7c11 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,6 @@
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
-int bam_pileup(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[]);
@@ -27,9 +26,12 @@ 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[]);
-int glf3_view_main(int argc, char *argv[]);
 
 static int usage()
 {
@@ -39,7 +41,6 @@ static int usage()
 	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, "         pileup      generate pileup output\n");
 	fprintf(stderr, "         mpileup     multi-way pileup\n");
 	fprintf(stderr, "         depth       compute the depth\n");
 	fprintf(stderr, "         faidx       index/extract FASTA\n");
@@ -49,15 +50,17 @@ static int usage()
 	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, "         glfview     print GLFv3 file\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, "\
@@ -80,7 +83,6 @@ int main(int argc, char *argv[])
 	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], "pileup") == 0) return bam_pileup(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);
@@ -89,7 +91,6 @@ int main(int argc, char *argv[])
 	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], "glfview") == 0) return glf3_view_main(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);
@@ -98,6 +99,15 @@ int main(int argc, char *argv[])
 	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