add new files

[rsem.git] / sam_rsem_aux.h

diff --git a/sam_rsem_aux.h b/sam_rsem_aux.h
new file mode 100644 (file)
index 0000000..5b4f9cd
--- /dev/null
+++ b/sam_rsem_aux.h
@@ -0,0 +1,48 @@
+#ifndef SAM_RSEM_AUX_H_
+#define SAM_RSEM_AUX_H_
+
+#include<cstdio>
+#include<cstring>
+#include<stdint.h>
+
+#include "sam/bam.h"
+
+// dwt: duplicate without text
+bam_header_t *bam_header_dwt(const bam_header_t *ori_h)
+{
+       bam_header_t *h;
+
+       h = bam_header_init();
+       h->n_targets = ori_h->n_targets;
+       h->target_len = (uint32_t*)calloc(h->n_targets, 4);
+       h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
+       for (int i = 0; i < h->n_targets; i++) {
+               h->target_len[i] = ori_h->target_len[i];
+               h->target_name[i] = strdup(ori_h->target_name[i]);
+       }
+
+       return h;
+}
+
+void append_header_text(bam_header_t *header, const char* text, int len)
+{
+       int x = header->l_text + 1;
+       int y = header->l_text + len + 1; // 1 byte null
+       if (text == 0) return;
+       kroundup32(x);
+       kroundup32(y);
+       if (x < y) header->text = (char*)realloc(header->text, y);
+       strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
+       header->l_text += len;
+       header->text[header->l_text] = 0;
+}
+
+void expand_data_size(bam1_t *b) {
+       if (b->m_data < b->data_len) {
+               b->m_data = b->data_len;
+               kroundup32(b->m_data);
+               b->data = (uint8_t*)realloc(b->data, b->m_data);
+       }
+}
+
+#endif /* SAM_RSEM_AUX_H_ */