--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bam_cat.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,185 @@
+/*
+
+bam_cat -- efficiently concatenates bam files
+
+bam_cat can be used to concatenate BAM files. Under special
+circumstances, it can be used as an alternative to 'samtools merge' to
+concatenate multiple sorted files into a single sorted file. For this
+to work each file must be sorted, and the sorted files must be given
+as command line arguments in order such that the final read in file i
+is less than or equal to the first read in file i+1.
+
+This code is derived from the bam_reheader function in samtools 0.1.8
+and modified to perform concatenation by Chris Saunders on behalf of
+Illumina.
+
+
+########## License:
+
+The MIT License
+
+Original SAMtools work copyright (c) 2008-2009 Genome Research Ltd.
+Modified SAMtools work copyright (c) 2010 Illumina, Inc.
+
+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.
+
+*/
+
+
+/*
+makefile:
+"""
+CC=gcc
+CFLAGS+=-g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I$(SAMTOOLS_DIR)
+LDFLAGS+=-L$(SAMTOOLS_DIR)
+LDLIBS+=-lbam -lz
+
+all:bam_cat
+"""
+*/
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#include "knetfile.h"
+#include "bgzf.h"
+#include "bam.h"
+
+#define BUF_SIZE 0x10000
+
+#define GZIPID1 31
+#define GZIPID2 139
+
+#define BGZF_EMPTY_BLOCK_SIZE 28
+
+
+int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam)
+{
+    BGZF *fp;
+    FILE* fp_file;
+    uint8_t *buf;
+    uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE];
+    const int es=BGZF_EMPTY_BLOCK_SIZE;
+    int i;
+    
+    fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(stdout), "w");
+    if (fp == 0) {
+        fprintf(stderr, "[%s] ERROR: fail to open output file '%s'.\n", __func__, outbam);
+        return 1;
+    }
+    if (h) bam_header_write(fp, h);
+    
+    buf = (uint8_t*) malloc(BUF_SIZE);
+    for(i = 0; i < nfn; ++i){
+        BGZF *in;
+        bam_header_t *old;
+        int len,j;
+        
+        in = strcmp(fn[i], "-")? bam_open(fn[i], "r") : bam_dopen(fileno(stdin), "r");
+        if (in == 0) {
+            fprintf(stderr, "[%s] ERROR: fail to open file '%s'.\n", __func__, fn[i]);
+            return -1;
+        }
+        if (in->is_write) return -1;
+        
+        old = bam_header_read(in);
+		if (h == 0 && i == 0) bam_header_write(fp, old);
+        
+        if (in->block_offset < in->block_length) {
+            bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
+            bgzf_flush(fp);
+        }
+        
+        j=0;
+#ifdef _USE_KNETFILE
+        fp_file = fp->fp;
+        while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0) {
+#else  
+        fp_file = fp->fp;
+        while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) {
+#endif
+            if(len<es){
+                int diff=es-len;
+                if(j==0) {
+                    fprintf(stderr, "[%s] ERROR: truncated file?: '%s'.\n", __func__, fn[i]);
+                    return -1;
+                }
+                fwrite(ebuf, 1, len, fp_file);
+                memcpy(ebuf,ebuf+len,diff);
+                memcpy(ebuf+diff,buf,len);
+            } else {
+                if(j!=0) fwrite(ebuf, 1, es, fp_file);
+                len-= es;
+                memcpy(ebuf,buf+len,es);
+                fwrite(buf, 1, len, fp_file);
+            }
+            j=1;
+        }
+
+        /* check final gzip block */
+        {
+            const uint8_t gzip1=ebuf[0];
+            const uint8_t gzip2=ebuf[1];
+            const uint32_t isize=*((uint32_t*)(ebuf+es-4));
+            if(((gzip1!=GZIPID1) || (gzip2!=GZIPID2)) || (isize!=0)) {
+                fprintf(stderr, "[%s] WARNING: Unexpected block structure in file '%s'.", __func__, fn[i]);
+                fprintf(stderr, " Possible output corruption.\n");
+                fwrite(ebuf, 1, es, fp_file);
+            }
+        }
+        bam_header_destroy(old);
+        bgzf_close(in);
+    }
+    free(buf);
+    bgzf_close(fp);
+    return 0;
+}
+
+
+
+int main_cat(int argc, char *argv[])
+{
+    bam_header_t *h = 0;
+	char *outfn = 0;
+	int c, ret;
+	while ((c = getopt(argc, argv, "h:o:")) >= 0) {
+		switch (c) {
+			case 'h': {
+        		tamFile fph = sam_open(optarg);
+		        if (fph == 0) {
+    		        fprintf(stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, argv[1]);
+        		    return 1;
+	        	}
+	    	    h = sam_header_read(fph);
+    	    	sam_close(fph);
+				break;
+			}
+			case 'o': outfn = strdup(optarg); break;
+		}
+	}
+	if (argc - optind < 2) {
+        fprintf(stderr, "Usage: samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [...]\n");
+        return 1;
+    }
+    ret = bam_cat(argc - optind, argv + optind, h, outfn? outfn : "-");
+	free(outfn);
+	return ret;
+}