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| 1 | Package:·libhtsjdk-java-doc | 1 | Package:·libhtsjdk-java-doc |
| 2 | Source:·htsjdk | 2 | Source:·htsjdk |
| 3 | Version:·4.1.0+dfsg-1 | 3 | Version:·4.1.0+dfsg-1 |
| 4 | Architecture:·all | 4 | Architecture:·all |
| 5 | Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org> | 5 | Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org> |
| 6 | Installed-Size:·2514 | 6 | Installed-Size:·25147 |
| 7 | Section:·doc | 7 | Section:·doc |
| 8 | Priority:·optional | 8 | Priority:·optional |
| 9 | Multi-Arch:·foreign | 9 | Multi-Arch:·foreign |
| 10 | Homepage:·https://samtools.github.io/htsjdk/ | 10 | Homepage:·https://samtools.github.io/htsjdk/ |
| 11 | Description:·Documentation·for·the·java·HTSJDK·library | 11 | Description:·Documentation·for·the·java·HTSJDK·library |
| 12 | ·HTSJDK·is·an·implementation·of·a·unified·Java·library·for·accessing·common | 12 | ·HTSJDK·is·an·implementation·of·a·unified·Java·library·for·accessing·common |
| 13 | ·file·formats,·such·as·SAM·(Sequence·Alignment/Map)·and·VCF,·used·for | 13 | ·file·formats,·such·as·SAM·(Sequence·Alignment/Map)·and·VCF,·used·for |
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| 6667 | <div·class="block">Scans·the·classpath·for·classes·within·the·specified·package·and·sub-packages·that | 6667 | <div·class="block">Scans·the·classpath·for·classes·within·the·specified·package·and·sub-packages·that |
| 6668 | ·extend·the·parentType.</div> | 6668 | ·extend·the·parentType.</div> |
| 6669 | </dd> | 6669 | </dd> |
| 6670 | <dt><a·href="htsjdk/samtools/cram/CRAIIndex.html#find(java.util.List,int,int,int)"·class="member-name-link">find(List<CRAIEntry>,·int,·int,·int)</a>·-·Static·method·in·class·htsjdk.samtools.cram.<a·href="htsjdk/samtools/cram/CRAIIndex.html"·title="class·in·htsjdk.samtools.cram">CRAIIndex</a></dt> | 6670 | <dt><a·href="htsjdk/samtools/cram/CRAIIndex.html#find(java.util.List,int,int,int)"·class="member-name-link">find(List<CRAIEntry>,·int,·int,·int)</a>·-·Static·method·in·class·htsjdk.samtools.cram.<a·href="htsjdk/samtools/cram/CRAIIndex.html"·title="class·in·htsjdk.samtools.cram">CRAIIndex</a></dt> |
| 6671 | <dd> | 6671 | <dd> |
| 6672 | <div·class="block">Currently·unused,·but·retained·for·the·native·rai·query·implementation</div> | 6672 | <div·class="block">Currently·unused,·but·retained·for·the·native·rai·query·implementation</div> |
| 6673 | </dd> | 6673 | </dd> |
| 6674 | <dt><a·href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#findAndLoadSequenceDictionary(java.nio.file.Path)"·class="member-name-link">findAndLoadSequenceDictionary(Path)</a>·-·Method·in·class·htsjdk.samtools.reference.<a·href="htsjdk/samtools/reference/ | 6674 | <dt><a·href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#findAndLoadSequenceDictionary(java.nio.file.Path)"·class="member-name-link">findAndLoadSequenceDictionary(Path)</a>·-·Method·in·class·htsjdk.samtools.reference.<a·href="htsjdk/samtools/reference/BlockCompressedI[·...·truncated·by·diffoscope;·len:·88,·SHA:·44be62ca3aaa55627f4efebc6281393e1afa9131913e0e4e5a600ab2773a299c·...·]IndexedFastaSequenceFile</a></dt> |
| 6675 | <dd> | 6675 | <dd> |
| 6676 | <div·class="block">Attempts·to·find·and·load·the·sequence·dictionary·if·present.</div> | 6676 | <div·class="block">Attempts·to·find·and·load·the·sequence·dictionary·if·present.</div> |
| 6677 | </dd> | 6677 | </dd> |
| 6678 | <dt><a·href="htsjdk/samtools/util/IntervalTree.html#findByIndex(int)"·class="member-name-link">findByIndex(int)</a>·-·Method·in·class·htsjdk.samtools.util.<a·href="htsjdk/samtools/util/IntervalTree.html"·title="class·in·htsjdk.samtools.util">IntervalTree</a></dt> | 6678 | <dt><a·href="htsjdk/samtools/util/IntervalTree.html#findByIndex(int)"·class="member-name-link">findByIndex(int)</a>·-·Method·in·class·htsjdk.samtools.util.<a·href="htsjdk/samtools/util/IntervalTree.html"·title="class·in·htsjdk.samtools.util">IntervalTree</a></dt> |
| 6679 | <dd> | 6679 | <dd> |
| 6680 | <div·class="block">Find·the·nth·interval·in·the·tree.</div> | 6680 | <div·class="block">Find·the·nth·interval·in·the·tree.</div> |
| 6681 | </dd> | 6681 | </dd> |
| 6682 | <dt><a·href="htsjdk/samtools/SAMFlag.html#findByName(java.lang.String)"·class="member-name-link">findByName(String)</a>·-·Static·method·in·enum·class·htsjdk.samtools.<a·href="htsjdk/samtools/SAMFlag.html"·title="enum·class·in·htsjdk.samtools">SAMFlag</a></dt> | 6682 | <dt><a·href="htsjdk/samtools/SAMFlag.html#findByName(java.lang.String)"·class="member-name-link">findByName(String)</a>·-·Static·method·in·enum·class·htsjdk.samtools.<a·href="htsjdk/samtools/SAMFlag.html"·title="enum·class·in·htsjdk.samtools">SAMFlag</a></dt> |
| 6683 | <dd> </dd> | 6683 | <dd> </dd> |
| 6684 | <dt><a·href="htsjdk/samtools/reference/IndexedFastaSequenceFile.html#findFastaIndex(java.nio.file.Path)"·class="member-name-link">findFastaIndex(Path)</a>·-·Static·method·in·class·htsjdk.samtools.reference.<a·href="htsjdk/samtools/reference/IndexedFastaSequenceF | 6684 | <dt><a·href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html#findFastaIndex(java.nio.file.Path)"·class="member-name-link">findFastaIndex(Path)</a>·-·Static·method·in·class·htsjdk.samtools.reference.<a·href="htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile[·...·truncated·by·diffoscope;·len:·65,·SHA:·10808bda5d7d9467ebfa8ed6bd1c2ad6457b4e0ace51caac345459eda054e4a9·...·]IndexedFastaSequenceFile</a></dt> |
| 6685 | <dd> </dd> | 6685 | <dd> </dd> |
| 6686 | <dt><a·href="htsjdk/samtools/SamFiles.html#findIndex(java.io.File)"·class="member-name-link">findIndex(File)</a>·-·Static·method·in·class·htsjdk.samtools.<a·href="htsjdk/samtools/SamFiles.html"·title="class·in·htsjdk.samtools">SamFiles</a></dt> | 6686 | <dt><a·href="htsjdk/samtools/SamFiles.html#findIndex(java.io.File)"·class="member-name-link">findIndex(File)</a>·-·Static·method·in·class·htsjdk.samtools.<a·href="htsjdk/samtools/SamFiles.html"·title="class·in·htsjdk.samtools">SamFiles</a></dt> |
| 6687 | <dd> | 6687 | <dd> |
| 6688 | <div·class="block">Finds·the·index·file·associated·with·the·provided·SAM·file.</div> | 6688 | <div·class="block">Finds·the·index·file·associated·with·the·provided·SAM·file.</div> |
| 6689 | </dd> | 6689 | </dd> |
| 6690 | <dt><a·href="htsjdk/samtools/SamFiles.html#findIndex(java.nio.file.Path)"·class="member-name-link">findIndex(Path)</a>·-·Static·method·in·class·htsjdk.samtools.<a·href="htsjdk/samtools/SamFiles.html"·title="class·in·htsjdk.samtools">SamFiles</a></dt> | 6690 | <dt><a·href="htsjdk/samtools/SamFiles.html#findIndex(java.nio.file.Path)"·class="member-name-link">findIndex(Path)</a>·-·Static·method·in·class·htsjdk.samtools.<a·href="htsjdk/samtools/SamFiles.html"·title="class·in·htsjdk.samtools">SamFiles</a></dt> |
| 6691 | <dd> | 6691 | <dd> |
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| 5342 | ··_\x8f_\x8i_\x8n_\x8d_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8C_\x8l_\x8a_\x8s_\x8s_\x8<_\x8?_\x8>_\x8)·-·Method·in·class·htsjdk.utils._\x8C_\x8l_\x8a_\x8s_\x8s_\x8F_\x8i_\x8n_\x8d_\x8e_\x8r | 5342 | ··_\x8f_\x8i_\x8n_\x8d_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8C_\x8l_\x8a_\x8s_\x8s_\x8<_\x8?_\x8>_\x8)·-·Method·in·class·htsjdk.utils._\x8C_\x8l_\x8a_\x8s_\x8s_\x8F_\x8i_\x8n_\x8d_\x8e_\x8r |
| 5343 | ······Scans·the·classpath·for·classes·within·the·specified·package·and·sub- | 5343 | ······Scans·the·classpath·for·classes·within·the·specified·package·and·sub- |
| 5344 | ······packages·that·extend·the·parentType. | 5344 | ······packages·that·extend·the·parentType. |
| 5345 | ··_\x8f_\x8i_\x8n_\x8d_\x8(_\x8L_\x8i_\x8s_\x8t_\x8<_\x8C_\x8R_\x8A_\x8I_\x8E_\x8n_\x8t_\x8r_\x8y_\x8>_\x8,_\x8·_\x8i_\x8n_\x8t_\x8,_\x8·_\x8i_\x8n_\x8t_\x8,_\x8·_\x8i_\x8n_\x8t_\x8)·-·Static·method·in·class | 5345 | ··_\x8f_\x8i_\x8n_\x8d_\x8(_\x8L_\x8i_\x8s_\x8t_\x8<_\x8C_\x8R_\x8A_\x8I_\x8E_\x8n_\x8t_\x8r_\x8y_\x8>_\x8,_\x8·_\x8i_\x8n_\x8t_\x8,_\x8·_\x8i_\x8n_\x8t_\x8,_\x8·_\x8i_\x8n_\x8t_\x8)·-·Static·method·in·class |
| 5346 | ··htsjdk.samtools.cram._\x8C_\x8R_\x8A_\x8I_\x8I_\x8n_\x8d_\x8e_\x8x | 5346 | ··htsjdk.samtools.cram._\x8C_\x8R_\x8A_\x8I_\x8I_\x8n_\x8d_\x8e_\x8x |
| 5347 | ······Currently·unused,·but·retained·for·the·native·rai·query·implementation | 5347 | ······Currently·unused,·but·retained·for·the·native·rai·query·implementation |
| 5348 | ··_\x8f_\x8i_\x8n_\x8d_\x8A_\x8n_\x8d_\x8L_\x8o_\x8a_\x8d_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8D_\x8i_\x8c_\x8t_\x8i_\x8o_\x8n_\x8a_\x8r_\x8y_\x8(_\x8P_\x8a_\x8t_\x8h_\x8)·-·Method·in·class | 5348 | ··_\x8f_\x8i_\x8n_\x8d_\x8A_\x8n_\x8d_\x8L_\x8o_\x8a_\x8d_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8D_\x8i_\x8c_\x8t_\x8i_\x8o_\x8n_\x8a_\x8r_\x8y_\x8(_\x8P_\x8a_\x8t_\x8h_\x8)·-·Method·in·class |
| 5349 | ··htsjdk.samtools.reference._\x8I_\x8n_\x8d_\x8e_\x8x_\x8e_\x8d_\x8F_\x8a_\x8s_\x8t_\x8a_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8F_\x8i_\x8l_\x8e | 5349 | ··htsjdk.samtools.reference._\x8B_.l_.o_.c_.k_.C_.o_.m_.p_.r_.e_.s_.s_.e_.d_.I_\x8n_\x8d_\x8e_\x8x_\x8e_\x8d_\x8F_\x8a_\x8s_\x8t_\x8a_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8F_\x8i_\x8l_\x8e |
| 5350 | ······Attempts·to·find·and·load·the·sequence·dictionary·if·present. | 5350 | ······Attempts·to·find·and·load·the·sequence·dictionary·if·present. |
| 5351 | ··_\x8f_\x8i_\x8n_\x8d_\x8B_\x8y_\x8I_\x8n_\x8d_\x8e_\x8x_\x8(_\x8i_\x8n_\x8t_\x8)·-·Method·in·class·htsjdk.samtools.util._\x8I_\x8n_\x8t_\x8e_\x8r_\x8v_\x8a_\x8l_\x8T_\x8r_\x8e_\x8e | 5351 | ··_\x8f_\x8i_\x8n_\x8d_\x8B_\x8y_\x8I_\x8n_\x8d_\x8e_\x8x_\x8(_\x8i_\x8n_\x8t_\x8)·-·Method·in·class·htsjdk.samtools.util._\x8I_\x8n_\x8t_\x8e_\x8r_\x8v_\x8a_\x8l_\x8T_\x8r_\x8e_\x8e |
| 5352 | ······Find·the·nth·interval·in·the·tree. | 5352 | ······Find·the·nth·interval·in·the·tree. |
| 5353 | ··_\x8f_\x8i_\x8n_\x8d_\x8B_\x8y_\x8N_\x8a_\x8m_\x8e_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Static·method·in·enum·class·htsjdk.samtools._\x8S_\x8A_\x8M_\x8F_\x8l_\x8a_\x8g | 5353 | ··_\x8f_\x8i_\x8n_\x8d_\x8B_\x8y_\x8N_\x8a_\x8m_\x8e_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Static·method·in·enum·class·htsjdk.samtools._\x8S_\x8A_\x8M_\x8F_\x8l_\x8a_\x8g |
| 5354 | ······ | 5354 | ······ |
| 5355 | ··_\x8f_\x8i_\x8n_\x8d_\x8F_\x8a_\x8s_\x8t_\x8a_\x8I_\x8n_\x8d_\x8e_\x8x_\x8(_\x8P_\x8a_\x8t_\x8h_\x8)·-·Static·method·in·class | 5355 | ··_\x8f_\x8i_\x8n_\x8d_\x8F_\x8a_\x8s_\x8t_\x8a_\x8I_\x8n_\x8d_\x8e_\x8x_\x8(_\x8P_\x8a_\x8t_\x8h_\x8)·-·Static·method·in·class |
| 5356 | ··htsjdk.samtools.reference._\x8I_\x8n_\x8d_\x8e_\x8x_\x8e_\x8d_\x8F_\x8a_\x8s_\x8t_\x8a_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8F_\x8i_\x8l_\x8e | 5356 | ··htsjdk.samtools.reference._\x8B_.l_.o_.c_.k_.C_.o_.m_.p_.r_.e_.s_.s_.e_.d_.I_\x8n_\x8d_\x8e_\x8x_\x8e_\x8d_\x8F_\x8a_\x8s_\x8t_\x8a_\x8S_\x8e_\x8q_\x8u_\x8e_\x8n_\x8c_\x8e_\x8F_\x8i_\x8l_\x8e |
| 5357 | ······ | 5357 | ······ |
| 5358 | ··_\x8f_\x8i_\x8n_\x8d_\x8I_\x8n_\x8d_\x8e_\x8x_\x8(_\x8F_\x8i_\x8l_\x8e_\x8)·-·Static·method·in·class·htsjdk.samtools._\x8S_\x8a_\x8m_\x8F_\x8i_\x8l_\x8e_\x8s | 5358 | ··_\x8f_\x8i_\x8n_\x8d_\x8I_\x8n_\x8d_\x8e_\x8x_\x8(_\x8F_\x8i_\x8l_\x8e_\x8)·-·Static·method·in·class·htsjdk.samtools._\x8S_\x8a_\x8m_\x8F_\x8i_\x8l_\x8e_\x8s |
| 5359 | ······Finds·the·index·file·associated·with·the·provided·SAM·file. | 5359 | ······Finds·the·index·file·associated·with·the·provided·SAM·file. |
| 5360 | ··_\x8f_\x8i_\x8n_\x8d_\x8I_\x8n_\x8d_\x8e_\x8x_\x8(_\x8P_\x8a_\x8t_\x8h_\x8)·-·Static·method·in·class·htsjdk.samtools._\x8S_\x8a_\x8m_\x8F_\x8i_\x8l_\x8e_\x8s | 5360 | ··_\x8f_\x8i_\x8n_\x8d_\x8I_\x8n_\x8d_\x8e_\x8x_\x8(_\x8P_\x8a_\x8t_\x8h_\x8)·-·Static·method·in·class·htsjdk.samtools._\x8S_\x8a_\x8m_\x8F_\x8i_\x8l_\x8e_\x8s |
| 5361 | ······Finds·the·index·file·associated·with·the·provided·SAM·file. | 5361 | ······Finds·the·index·file·associated·with·the·provided·SAM·file. |
| 5362 | ··_\x8f_\x8i_\x8n_\x8d_\x8L_\x8a_\x8s_\x8t_\x8A_\x8l_\x8i_\x8g_\x8n_\x8e_\x8d_\x8E_\x8n_\x8t_\x8r_\x8y_\x8(_\x8L_\x8i_\x8s_\x8t_\x8<_\x8C_\x8R_\x8A_\x8I_\x8E_\x8n_\x8t_\x8r_\x8y_\x8>_\x8)·-·Static·method·in·class | 5362 | ··_\x8f_\x8i_\x8n_\x8d_\x8L_\x8a_\x8s_\x8t_\x8A_\x8l_\x8i_\x8g_\x8n_\x8e_\x8d_\x8E_\x8n_\x8t_\x8r_\x8y_\x8(_\x8L_\x8i_\x8s_\x8t_\x8<_\x8C_\x8R_\x8A_\x8I_\x8E_\x8n_\x8t_\x8r_\x8y_\x8>_\x8)·-·Static·method·in·class |
| 5363 | ··htsjdk.samtools.cram._\x8C_\x8R_\x8A_\x8I_\x8I_\x8n_\x8d_\x8e_\x8x | 5363 | ··htsjdk.samtools.cram._\x8C_\x8R_\x8A_\x8I_\x8I_\x8n_\x8d_\x8e_\x8x |
| Offset 8165, 29 lines modified | Offset 8165, 29 lines modified | ||
| 8165 | },·{ | 8165 | },·{ |
| 8166 | ····"p":·"htsjdk.utils", | 8166 | ····"p":·"htsjdk.utils", |
| 8167 | ····"c":·"ClassFinder", | 8167 | ····"c":·"ClassFinder", |
| 8168 | ····"l":·"find(String,·Class<?>)", | 8168 | ····"l":·"find(String,·Class<?>)", |
| 8169 | ····"u":·"find(java.lang.String,java.lang.Class)" | 8169 | ····"u":·"find(java.lang.String,java.lang.Class)" |
| 8170 | },·{ | 8170 | },·{ |
| 8171 | ····"p":·"htsjdk.samtools.reference", | 8171 | ····"p":·"htsjdk.samtools.reference", |
| 8172 | ····"c":·"IndexedFastaSequenceFile", | 8172 | ····"c":·"BlockCompressedIndexedFastaSequenceFile", |
| 8173 | ····"l":·"findAndLoadSequenceDictionary(Path)", | 8173 | ····"l":·"findAndLoadSequenceDictionary(Path)", |
| 8174 | ····"u":·"findAndLoadSequenceDictionary(java.nio.file.Path)" | 8174 | ····"u":·"findAndLoadSequenceDictionary(java.nio.file.Path)" |
| 8175 | },·{ | 8175 | },·{ |
| 8176 | ····"p":·"htsjdk.samtools.util", | 8176 | ····"p":·"htsjdk.samtools.util", |
| 8177 | ····"c":·"IntervalTree", | 8177 | ····"c":·"IntervalTree", |
| 8178 | ····"l":·"findByIndex(int)" | 8178 | ····"l":·"findByIndex(int)" |
| 8179 | },·{ | 8179 | },·{ |
| 8180 | ····"p":·"htsjdk.samtools", | 8180 | ····"p":·"htsjdk.samtools", |
| 8181 | ····"c":·"SAMFlag", | 8181 | ····"c":·"SAMFlag", |
| 8182 | ····"l":·"findByName(String)", | 8182 | ····"l":·"findByName(String)", |
| 8183 | ····"u":·"findByName(java.lang.String)" | 8183 | ····"u":·"findByName(java.lang.String)" |
| 8184 | },·{ | 8184 | },·{ |
| 8185 | ····"p":·"htsjdk.samtools.reference", | 8185 | ····"p":·"htsjdk.samtools.reference", |
| 8186 | ····"c":·"IndexedFastaSequenceFile", | 8186 | ····"c":·"BlockCompressedIndexedFastaSequenceFile", |
| 8187 | ····"l":·"findFastaIndex(Path)", | 8187 | ····"l":·"findFastaIndex(Path)", |
| 8188 | ····"u":·"findFastaIndex(java.nio.file.Path)" | 8188 | ····"u":·"findFastaIndex(java.nio.file.Path)" |
| 8189 | },·{ | 8189 | },·{ |
| 8190 | ····"p":·"htsjdk.samtools", | 8190 | ····"p":·"htsjdk.samtools", |
| 8191 | ····"c":·"SamFiles", | 8191 | ····"c":·"SamFiles", |
| 8192 | ····"l":·"findIndex(File)", | 8192 | ····"l":·"findIndex(File)", |
| 8193 | ····"u":·"findIndex(java.io.File)" | 8193 | ····"u":·"findIndex(java.io.File)" |