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  1. <table style="width:100%;height:100%" , border="solid">
  2. <tr>
  3. <td>
  4. <p style="text-align: center;"><b>Field</b></p>
  5. </td>
  6. <td>
  7. <p style="text-align: center;"><b>Description</b></p>
  8. </td>
  9. <td>
  10. <p style="text-align: center;"><b>Type</b></p>
  11. </td>
  12. </tr>
  13. <tr>
  14. <td>magic</td>
  15. <td>CBAM magic string</td>
  16. <td>char[4]</td>
  17. </tr>
  18. <tr>
  19. <td colspan="3" valign="bottom" , align="right" style="height:100%">
  20. <p style="text-align: center;">
  21. <font color="gray">List of RowGroups</font>
  22. </p>
  23. <table style="width:95%;height:96%" , border="solid" align="right">
  24. <tr>
  25. <td>refID</td>
  26. <td>array of refID values of records in this rowgroup</td>
  27. <td>int[]</td>
  28. </tr>
  29. <tr>
  30. <td>pos</td>
  31. <td>array of pos values of records in this rowgroup</td>
  32. <td>int[]</td>
  33. </tr>
  34. <tr>
  35. <td>_blob_size</td>
  36. <td>array of refID values of records in this rowgroup</td>
  37. <td>int[]</td>
  38. </tr>
  39. <tr>
  40. <td>_bin_mq_nl</td>
  41. <td>array of bin_mq_nl byte arrays of records in this rowgroup</td>
  42. <td>byte[][]</td>
  43. </tr>
  44. <tr>
  45. <td>flag_nc</td>
  46. <td>array of flag_nc byte arrays of records in this rowgroup</td>
  47. <td>byte[][]</td>
  48. </tr>
  49. <tr>
  50. <td>sequence_length</td>
  51. <td>array of sequence_length byte arrays of records in this rowgroup</td>
  52. <td>byte[][]</td>
  53. </tr>
  54. <tr>
  55. <td>next_refID</td>
  56. <td>array of next_refID byte arrays of records in this rowgroup</td>
  57. <td nowrap>byte[][]</td>
  58. </tr>
  59. <tr>
  60. <td>next_pos</td>
  61. <td>array of next_pos byte arrays of records in this rowgroup</td>
  62. <td>byte[][]</td>
  63. </tr>
  64. <tr>
  65. <td>tlen</td>
  66. <td>array of tlen byte arrays of records in this rowgroup</td>
  67. <td>byte[][]</td>
  68. </tr>
  69. <tr>
  70. <td>read_name</td>
  71. <td>array of read_name byte arrays of records in this rowgroup. Each record has its length of type
  72. int written in front of byte array</td>
  73. <td>byte[][]</td>
  74. </tr>
  75. <tr>
  76. <td>read_name</td>
  77. <td>array of read_name byte arrays of records in this rowgroup. Each record has its length of type
  78. int written in front of byte array</td>
  79. <td>byte[][]</td>
  80. </tr>
  81. <tr>
  82. <td>raw_cigar</td>
  83. <td>array of raw_cigar byte arrays of records in this rowgroup. Each record has its length of type
  84. int written in front of byte array</td>
  85. <td>byte[][]</td>
  86. </tr>
  87. <tr>
  88. <td>raw_sequence</td>
  89. <td>array of raw_sequence byte arrays of records in this rowgroup. Each record has its length of
  90. type
  91. int written in front of byte array</td>
  92. <td>byte[][]</td>
  93. </tr>
  94. <tr>
  95. <td>raw_qual</td>
  96. <td>array of raw_qual byte arrays of records in this rowgroup. Each record has its length of type
  97. int written in front of byte array</td>
  98. <td>byte[][]</td>
  99. </tr>
  100. <tr>
  101. <td>raw_tags</td>
  102. <td>array of raw_tags byte arrays of records in this rowgroup. Each record has its length of type
  103. int written in front of byte array</td>
  104. <td>byte[][]</td>
  105. </tr>
  106. </table>
  107. </td>
  108. </tr>
  109. <tr>
  110. <td colspan="3" valign="bottom" , align="right" style="height:100%;">
  111. <p style="text-align: center;">
  112. <font color="gray">List of RowGroupMetas</font>
  113. </p>
  114. <table style="width:95%;height:80%" , border="solid" align="right">
  115. <tr>
  116. <td>columnsOffsets</td>
  117. <td>array of columns offsets in this rowgroup</td>
  118. <td>long[]</td>
  119. </tr>
  120. <tr>
  121. <td>columnsSizes</td>
  122. <td>array of columns sizes in this rowgroup</td>
  123. <td>long[]</td>
  124. </tr>
  125. <tr>
  126. <td>uncompressedColSizes</td>
  127. <td>array of uncompressed columns sizes in this rowgroup</td>
  128. <td>long[]</td>
  129. </tr>
  130. <tr>
  131. <td>total_byte_size</td>
  132. <td>size in bytes of this rowgroup</td>
  133. <td>long</td>
  134. </tr>
  135. <tr>
  136. <td>num_rows</td>
  137. <td>amount of records in this rowgroup</td>
  138. <td>int</td>
  139. </tr>
  140. </table>
  141. </td>
  142. </tr>
  143. <tr>
  144. <td>textSize</td>
  145. <td>size of BamHeader text</td>
  146. <td>int</td>
  147. </tr>
  148. <tr>
  149. <td>bamText</td>
  150. <td>BamHeader text</td>
  151. <td>byte[]</td>
  152. </tr>
  153. <tr>
  154. <td>refsNum</td>
  155. <td>amount of reference sequences in BamHeader</td>
  156. <td>int</td>
  157. </tr>
  158. <tr>
  159. <td colspan="3" valign="bottom" , align="right" style="height:100%">
  160. <p style="text-align: center;">
  161. <font color="gray">List of Reference Sequences meta</font>
  162. </p>
  163. <table style="width:95%;height:70%" , border="solid" align="right">
  164. <tr>
  165. <td>refNameLength</td>
  166. <td>reference sequence name length</td>
  167. <td>int</td>
  168. </tr>
  169. <tr>
  170. <td>refName</td>
  171. <td>reference sequence name</td>
  172. <td>byte[]</td>
  173. </tr>
  174. <tr>
  175. <td>refLength</td>
  176. <td>reference sequence length</td>
  177. <td>long</td>
  178. </tr>
  179. </table>
  180. </td>
  181. </tr>
  182. <tr>
  183. <td>metaOffset</td>
  184. <td>Offset to fileMeta from end of CBAM file</td>
  185. <td>long</td>
  186. </tr>
  187. <tr>
  188. <td>metaSize</td>
  189. <td>fileMeta size</td>
  190. <td>int</td>
  191. </tr>
  192. <tr>
  193. <td>magic</td>
  194. <td>CBAM magic string</td>
  195. <td>char[4]</td>
  196. </tr>
  197. </table>