hs-samtools-0.2.0.1: Read and write SAM, BAM, and CRAM files.

Index

SAM_V1_6 
1 (Type/Class)Data.SAM.Version1_6.Internal
2 (Data Constructor)Data.SAM.Version1_6.Internal
SAM_V1_6_File_Level_Metadata 
1 (Type/Class)Data.SAM.Version1_6.Header.HD
2 (Data Constructor)Data.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadataData.SAM.Version1_6.Internal
SAM_V1_6_File_Level_Metadata_Alignment_Grouping 
1 (Type/Class)Data.SAM.Version1_6.Header.HD
2 (Data Constructor)Data.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_alignment_groupingData.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_alignment_grouping_tagData.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_alignment_grouping_valueData.SAM.Version1_6.Header.HD
SAM_V1_6_File_Level_Metadata_Format_Version 
1 (Type/Class)Data.SAM.Version1_6.Header.HD
2 (Data Constructor)Data.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_format_versionData.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_format_version_tagData.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_format_version_valueData.SAM.Version1_6.Header.HD
SAM_V1_6_File_Level_Metadata_Sorting_Order 
1 (Type/Class)Data.SAM.Version1_6.Header.HD
2 (Data Constructor)Data.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_sorting_orderData.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_sorting_order_tagData.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_sorting_order_valueData.SAM.Version1_6.Header.HD
SAM_V1_6_File_Level_Metadata_SubSorting_Order 
1 (Type/Class)Data.SAM.Version1_6.Header.HD
2 (Data Constructor)Data.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_subsorting_orderData.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_subsorting_order_tagData.SAM.Version1_6.Header.HD
sam_v1_6_file_level_metadata_subsorting_order_valueData.SAM.Version1_6.Header.HD
SAM_V1_6_One_Line_Comment 
1 (Type/Class)Data.SAM.Version1_6.Header.CO
2 (Data Constructor)Data.SAM.Version1_6.Header.CO
sam_v1_6_one_line_commentData.SAM.Version1_6.Internal
sam_v1_6_one_line_comment_tagData.SAM.Version1_6.Header.CO
sam_v1_6_one_line_comment_valueData.SAM.Version1_6.Header.CO
SAM_V1_6_Program 
1 (Type/Class)Data.SAM.Version1_6.Header.PG
2 (Data Constructor)Data.SAM.Version1_6.Header.PG
sam_v1_6_programData.SAM.Version1_6.Internal
SAM_V1_6_Program_Command_Line 
1 (Type/Class)Data.SAM.Version1_6.Header.PG
2 (Data Constructor)Data.SAM.Version1_6.Header.PG
sam_v1_6_program_command_lineData.SAM.Version1_6.Header.PG
sam_v1_6_program_command_line_tagData.SAM.Version1_6.Header.PG
sam_v1_6_program_command_line_valueData.SAM.Version1_6.Header.PG
SAM_V1_6_Program_Description 
1 (Type/Class)Data.SAM.Version1_6.Header.PG
2 (Data Constructor)Data.SAM.Version1_6.Header.PG
sam_v1_6_program_descriptionData.SAM.Version1_6.Header.PG
sam_v1_6_program_description_tagData.SAM.Version1_6.Header.PG
sam_v1_6_program_description_valueData.SAM.Version1_6.Header.PG
SAM_V1_6_Program_Name 
1 (Type/Class)Data.SAM.Version1_6.Header.PG
2 (Data Constructor)Data.SAM.Version1_6.Header.PG
sam_v1_6_program_nameData.SAM.Version1_6.Header.PG
sam_v1_6_program_name_tagData.SAM.Version1_6.Header.PG
sam_v1_6_program_name_valueData.SAM.Version1_6.Header.PG
SAM_V1_6_Program_Previous_PG_ID 
1 (Type/Class)Data.SAM.Version1_6.Header.PG
2 (Data Constructor)Data.SAM.Version1_6.Header.PG
sam_v1_6_program_previous_pg_idData.SAM.Version1_6.Header.PG
sam_v1_6_program_previous_pg_id_tagData.SAM.Version1_6.Header.PG
sam_v1_6_program_previous_pg_id_valueData.SAM.Version1_6.Header.PG
SAM_V1_6_Program_Record_Identifier 
1 (Type/Class)Data.SAM.Version1_6.Header.PG
2 (Data Constructor)Data.SAM.Version1_6.Header.PG
sam_v1_6_program_record_identifierData.SAM.Version1_6.Header.PG
sam_v1_6_program_record_identifier_tagData.SAM.Version1_6.Header.PG
sam_v1_6_program_record_identifier_valueData.SAM.Version1_6.Header.PG
SAM_V1_6_Program_Version 
1 (Type/Class)Data.SAM.Version1_6.Header.PG
2 (Data Constructor)Data.SAM.Version1_6.Header.PG
sam_v1_6_program_versionData.SAM.Version1_6.Header.PG
sam_v1_6_program_version_tagData.SAM.Version1_6.Header.PG
sam_v1_6_program_version_valueData.SAM.Version1_6.Header.PG
SAM_V1_6_Read_Group 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_groupData.SAM.Version1_6.Internal
SAM_V1_6_Read_Group_Barcode_Sequence 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_barcode_sequenceData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_barcode_sequence_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_barcode_sequence_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Description 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_descriptionData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_description_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_description_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Flow_Order 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_flow_orderData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_flow_order_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_flow_order_valueData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_identiferData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_identifer_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_identifer_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Identifier 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Key_Sequence 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_key_sequenceData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_key_sequence_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_key_sequence_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Library 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_libraryData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_library_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_library_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Platform 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platformData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Platform_Model 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platform_modelData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platform_model_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platform_model_valueData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platform_tagData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Platform_Unit 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platform_unitData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platform_unit_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platform_unit_valueData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_platform_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Predicted_Median_Insert_Size 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_predicted_median_insert_sizeData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_predicted_median_insert_size_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_predicted_median_insert_size_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Programs 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_programsData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_programs_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_programs_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Run_Date 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_run_dateData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_run_date_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_run_date_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Sample 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_sampleData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_sample_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_sample_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Read_Group_Sequencing_Center 
1 (Type/Class)Data.SAM.Version1_6.Header.RG
2 (Data Constructor)Data.SAM.Version1_6.Header.RG
sam_v1_6_read_group_sequencing_centerData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_sequencing_center_tagData.SAM.Version1_6.Header.RG
sam_v1_6_read_group_sequencing_center_valueData.SAM.Version1_6.Header.RG
SAM_V1_6_Reference_Sequence_Dictionary 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionaryData.SAM.Version1_6.Internal
SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_Description 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_descriptionData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_description_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_description_valueData.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_genome_assembly_identifierData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_valueData.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_md5_checksumData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_md5_checksum_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_md5_checksum_valueData.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_molecule_topologyData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_molecule_topology_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_molecule_topology_valueData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_alternative_locusData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_alternative_locus_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_alternative_locus_valueData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_namesData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names_valueData.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_sequence_lengthData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_sequence_length_valueData.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_sequence_nameData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_reference_sequence_name_valueData.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_Species 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_speciesData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_species_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_species_valueData.SAM.Version1_6.Header.SQ
SAM_V1_6_Reference_Sequence_Dictionary_URI 
1 (Type/Class)Data.SAM.Version1_6.Header.SQ
2 (Data Constructor)Data.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_uriData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_uri_tagData.SAM.Version1_6.Header.SQ
sam_v1_6_reference_sequence_dictionary_uri_valueData.SAM.Version1_6.Header.SQ