annotate ezBAMQC/src/htslib/cram/string_alloc.c @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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1 /*
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2 Copyright (c) 2010 Genome Research Ltd.
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3 Author: Andrew Whitwham <aw7@sanger.ac.uk>
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4
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5 Redistribution and use in source and binary forms, with or without
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6 modification, are permitted provided that the following conditions are met:
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7
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8 1. Redistributions of source code must retain the above copyright notice,
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9 this list of conditions and the following disclaimer.
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10
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11 2. Redistributions in binary form must reproduce the above copyright notice,
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12 this list of conditions and the following disclaimer in the documentation
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13 and/or other materials provided with the distribution.
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14
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15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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16 Institute nor the names of its contributors may be used to endorse or promote
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17 products derived from this software without specific prior written permission.
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18
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19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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29 */
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30
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31
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32 /*
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33 A pooled string allocator intended to cut down on the
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34 memory overhead of many small string allocations.
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35
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36 Andrew Whitwham, September 2010.
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37 */
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38
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39 #include <string.h>
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40 #include <stdlib.h>
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41 #include <stdio.h>
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42
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43 #include "string_alloc.h"
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44
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45 #define MIN_STR_SIZE 1024
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46
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47
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48 /* creates the string pool. max_length is the initial size
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49 a single string can be. Tha max_length can grow as
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50 needed */
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51
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52 string_alloc_t *string_pool_create(size_t max_length) {
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53 string_alloc_t *a_str;
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54
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55 if (NULL == (a_str = (string_alloc_t *)malloc(sizeof(*a_str)))) {
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56 return NULL;
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57 }
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58
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59 if (max_length < MIN_STR_SIZE) max_length = MIN_STR_SIZE;
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60
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61 a_str->nstrings = 0;
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62 a_str->max_length = max_length;
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63 a_str->strings = NULL;
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64
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65 return a_str;
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66 }
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67
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68
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69 /* internal function to do the actual memory allocation */
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70
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71 static string_t *new_string_pool(string_alloc_t *a_str) {
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72 string_t *str;
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73
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74 str = realloc(a_str->strings, (a_str->nstrings + 1) * sizeof(*a_str->strings));
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75
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76 if (NULL == str) return NULL;
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77
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78 a_str->strings = str;
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79 str = &a_str->strings[a_str->nstrings];
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80
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81 str->str = malloc(a_str->max_length);;
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82
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83 if (NULL == str->str) return NULL;
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84
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85 str->used = 0;
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86 a_str->nstrings++;
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87
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88 return str;
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89 }
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90
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91
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92 /* free allocated memory */
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93
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94 void string_pool_destroy(string_alloc_t *a_str) {
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95 size_t i;
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96
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97 for (i = 0; i < a_str->nstrings; i++) {
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98 free(a_str->strings[i].str);
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99 }
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100
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101 free(a_str->strings);
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102 free(a_str);
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103 }
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104
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105
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106 /* allocate space for a string */
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107
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108 char *string_alloc(string_alloc_t *a_str, size_t length) {
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109 string_t *str;
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110 char *ret;
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111
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112 if (length <= 0) return NULL;
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113
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114 // add to last string pool if we have space
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115 if (a_str->nstrings) {
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116 str = &a_str->strings[a_str->nstrings - 1];
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117
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118 if (str->used + length < a_str->max_length) {
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119 ret = str->str + str->used;
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120 str->used += length;
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121 return ret;
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122 }
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123 }
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124
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125 // increase the max length if needs be
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126 if (length > a_str->max_length) a_str->max_length = length;
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127
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128 // need a new string pool
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129 str = new_string_pool(a_str);
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130
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131 if (NULL == str) return NULL;
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132
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133 str->used = length;
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134 return str->str;
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135 }
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136
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137
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138 /* equivalent to strdup */
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139
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140 char *string_dup(string_alloc_t *a_str, char *instr) {
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141 return string_ndup(a_str, instr, strlen(instr));
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142 }
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143
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144 char *string_ndup(string_alloc_t *a_str, char *instr, size_t len) {
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145 char *str = string_alloc(a_str, len + 1);
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146
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147 if (NULL == str) return NULL;
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148
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149 strncpy(str, instr, len);
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150 str[len] = 0;
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151
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152 return str;
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153 }