h*`CP       !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~                                                                           !"#$%&'()*+,------.///////000000000000000000000000000000000000000000000000000000000000000000001111111222222233333334444444555555555556666666666666666677777788888888888888888888888888888888899999999999999999999999999999999999999999999999:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<<<<<<<<<<=================================================================== = = = = = = = = = = = = = = = = = = = = = > ? @ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z [ \ ] ^ _ ` a b c d e f g h i j k l mn0.10.0.2(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7< hs-samtoolsCustom BAM (version 1.6) &BAM_V1_6_Alignment_OptionalFields_AOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<  hs-samtoolsSum type that can represent any of the BAM_V1_6_BAM_Alignment_OptionalFields_BOPT types. hs-samtoolscCsSiIf% of the last optional field (type B).See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolscCsSiI&f of the last optional field (type B).See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolscCsSi'If of the last optional field (type B).See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation." hs-samtoolscCsS(iIf of the last optional field (type B).See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.( hs-samtoolscCs)SiIf of the last optional field (type B).See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.. hs-samtoolscC*sSiIf of the last optional field (type B).See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.4 hs-samtoolsc+CsSiIf of the last optional field (type B).See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.: hs-samtoolsCustom BAM (version 1.6) *BAM_V1_6_BAM_Alignment_OptionalFields_BOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.<:;<=>?@AB456789./0123()*+,-"#$%&' ! <:;<=>?@AB456789./0123()*+,-"#$%&' ! (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<!] hs-samtoolsCustom BAM (version 1.6) )BAM_V1_6_Alignment_OptionalFields_BigCOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.]^_`]^_`(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<"d hs-samtoolsCustom BAM (version 1.6) -BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.defgdefg(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<$Jk hs-samtoolsCustom BAM (version 1.6) )BAM_V1_6_Alignment_OptionalFields_BigSOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.klmnklmn(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<%r hs-samtoolsCustom BAM (version 1.6) &BAM_V1_6_Alignment_OptionalFields_FOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.rsturstu(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<'y hs-samtoolsCustom BAM (version 1.6) &BAM_V1_6_Alignment_OptionalFields_HOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.yz{|yz{|(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<(m hs-samtoolsCustom BAM (version 1.6) +BAM_V1_6_Alignment_OptionalFields_SmallCOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<) hs-samtoolsCustom BAM (version 1.6) /BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<+K hs-samtoolsCustom BAM (version 1.6) +BAM_V1_6_Alignment_OptionalFields_SmallSOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<, hs-samtoolsCustom BAM (version 1.6) &SAM_V1_6_Alignment_OptionalFields_ZOPT data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<18  hs-samtoolsSum type that can represent any of the BAM_V1_6_BAM_Alignment_OptionalFields types. hs-samtoolsCustom BAM (version 1.6) &BAM_V1_6_BAM_Alignment_Optional_Fields data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtools!A - [!-~] - Printable character. hs-samtoolsc - [0-9]+ - Int8 (signed). hs-samtoolsC - [0-9]+ - Word8 (unsigned). hs-samtoolsi - [0-9]+ - Int32 (signed). hs-samtools I - [0-9]+ - Word32 (unsigned). hs-samtoolss - [0-9]+ - Int16 (signed). hs-samtools S - [0-9]+ - Word16 (unsigned). hs-samtoolsf - [-+]?[0-9]*.?[0-9]+([eE][-+]?[0-9]+)? - Single-precision floating number. hs-samtools1Z - [ !-~]* - Printable string, including space. hs-samtools8H - ([0-9A-F][0-9A-F])* - Byte array in the Hex format. hs-samtoolsB - [cCsSiIf]@(,[-+]?[0-9]*.?[0-9]+([eE][-+]?[0-9]+)?)* - Integer or numeric array. (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<7@ hs-samtoolsCustom BAM (version 1.6) BAM_V1_6_BAM_Alignment data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtools '012345678'. hs-samtools4-bit encoded read: '=ACMGRSVTWYHKDBN' -> [0,15]. See section 4.2.3. hs-samtools0Phred-scaled base qualities. See section 4.2.3. hs-samtools+List of auxiliary data. See section 4.2.4o(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred 8(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<9 hs-samtoolsCustom BAM_V1_6_BAM_BAMAlignments (BAM version 1.6) data type.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsList of alignments.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<: hs-samtoolsCustom BAM (version 1.6) SAM_V1_6_One_Line_Comment data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<=J hs-samtools SS tag for BAM_V1_6_File_Level_Metadata. hs-samtools GO tag for BAM_V1_6_File_Level_Metadata. hs-samtools SO tag for BAM_V1_6_File_Level_Metadata. hs-samtools VN tag for BAM_V1_6_File_Level_Metadata. hs-samtoolsCustom BAM (version 1.6) BAM_V1_6_File_Level_Metadata data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<@ hs-samtools VN tag for BAM_V1_6_Program. hs-samtools DS tag for BAM_V1_6_Program. hs-samtools PP tag for BAM_V1_6_Program. hs-samtools CL tag for BAM_V1_6_Program. hs-samtools PN tag for BAM_V1_6_Program. hs-samtools ID tag for BAM_V1_6_Program. hs-samtoolsCustom BAM (version 1.6) BAM_V1_6_Program data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<D hs-samtools SM tag for BAM_V1_6_Read_Group. hs-samtools PU tag for BAM_V1_6_Read_Group. hs-samtools PM tag for BAM_V1_6_Read_Group. hs-samtools PL tag for BAM_V1_6_Read_Group. hs-samtools PI tag for BAM_V1_6_Read_Group. hs-samtools PG tag for BAM_V1_6_Read_Group. hs-samtools LB tag for BAM_V1_6_Read_Group. hs-samtools KS tag for BAM_V1_6_Read_Group. hs-samtools FO tag for BAM_V1_6_Read_Group. hs-samtools DT tag for BAM_V1_6_Read_Group. hs-samtools DS tag for BAM_V1_6_Read_Group. hs-samtools CN tag for BAM_V1_6_Read_Group. hs-samtools BC tag for BAM_V1_6_Read_Group. hs-samtools ID tag for BAM_V1_6_Read_Group. hs-samtoolsCustom BAM (version 1.6) BAM_V1_6_Read_Group data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.::(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<J9  hs-samtools UR tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools TP tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools SP tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools M5 tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools DS tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools AS tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools AN tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools AH tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools LN tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtools SN tag for &BAM_V1_6_Reference_Sequence_Dictionary. hs-samtoolsCustom BAM (version 1.6) &BAM_V1_6_Reference_Sequence_Dictionary data type.See section 4.2 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.**p(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred KY(c) Matthew Mosior 2023 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<N{ hs-samtoolsCustom "BAM_V1_6_BAM_Reference_Information (BAM version 1.6) data type.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtools4Length of the reference name plus 1 (including NUL). hs-samtools(Reference sequence name; NUL terminated. hs-samtools!Length of the reference sequence.q(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred O(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<Q hs-samtoolsCustom BAM_V1_6_BAM_BAMHeader (BAM version 1.6) data type.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtools/BAM magic string (magic). This should be BAM1. hs-samtools>Length of the header text, including any NUL padding (l_text). hs-samtools:Plain header text in SAM; not necessarily NUL-terminated. hs-samtools&Number of reference sequences (n_ref). hs-samtools7List of reference information (n = bam_v1_6_bam_n_ref).(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<R hs-samtoolsCustom  BAM_V1_6_BAM (BAM version 1.6) data type.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<U  hs-samtoolsCustom BAM_V1_6_GZipHeader (BAM version 1.6) data type.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsMagic number 1f (0x1f). hs-samtoolsMagic number 08 (0x08). hs-samtools$Compression method (08 for DEFLATE). hs-samtools1-byte for header flags. hs-samtools4-byte timestamp. hs-samtools1-byte eXtra FLags. hs-samtoolsThe operating system id. hs-samtoolsIf FLG.FEXTRA is set, this gives the length of the optional extra field.  (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<Z  hs-samtoolsCustom BAM_V1_6_BGZFBlock (BAM version 1.6) data type.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsGZip 10 byte header. This contains a magic number (1f 08), the compression method (08 for DEFLATE), 1-byte of header flags, a 4-byte timestamp, compression flags, and the operating system ID. hs-samtoolsThis should be B. hs-samtoolsThis should be  . hs-samtoolsThis should be '02 00'. hs-samtoolsThe payload of the BGZF extra field is a 16-bit unsigned integer in little endian format. This integer gives the size of the containing BGZF block minus one. hs-samtoolsCompressed DATA by zlib::deflate(). The data in this field will be in a decompressed and useable state. hs-samtoolsCRC-32. hs-samtools)Input SIZE (length of uncompressed data).  (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<[ hs-samtoolsCustom BAM_V1_6 (BAM version 1.6) newtype.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtools?Sequence holding all BGZF blocks of data within the BAM file.r(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferredb  hs-samtoolsConvert a Word16 in little endian byte order to a ByteString.  hs-samtools>Convert a Word32 in little endian byte order to a ByteString.  hs-samtools;Convert a Int in little endian byte order to a ByteString.  hs-samtools8Convert an Int in little-endian byte order to a Word16.  hs-samtools5Convert an Int little-endian byte order to a Word32.  hs-samtoolsSmallCOPT tag of the alignment section not in accepted format. hs-samtools?SmallCOPT type of the alignment section not in accepted format. hs-samtools>SmallIOPT tag of the alignment section not in accepted format. hs-samtools?SmallIOPT type of the alignment section not in accepted format. hs-samtools>SmallSOPT tag of the alignment section not in accepted format. hs-samtools?SmallSOPT type of the alignment section not in accepted format. hs-samtools9FOPT tag of the alignment section not in accepted format. hs-samtools:FOPT type of the alignment section not in accepted format. hs-samtools;FOPT value of the alignment section not in accepted format. hs-samtools9ZOPT tag of the alignment section not in accepted format. hs-samtools:ZOPT type of the alignment section not in accepted format. hs-samtools;ZOPT value of the alignment section not in accepted format. hs-samtools9HOPT tag of the alignment section not in accepted format. hs-samtools:HOPT type of the alignment section not in accepted format. hs-samtools;HOPT value of the alignment section not in accepted format. hs-samtools9BOPT tag of the alignment section not in accepted format. hs-samtools:BOPT type of the alignment section not in accepted format. hs-samtoolsBOPT value type of the alignment section not in accepted format. hs-samtoolsBOPT value data of the alignment section not in accepted format. hs-samtools7The CDATA field of a BGZF block not in accepted format. hs-samtoolsA CDATA BAM block alignment optional fields are not in accepted format. hs-samtoolsCRC-32 (CRC32) field of the GZip header not in accepted format. hs-samtoolsInput Size (Input SIZE, i.e. length of uncompressed data) not in accepted format. hs-samtoolsThe calculated crc32 of the uncompressed CDATA is not equivalent to the CRC32 field of the BGZF block. hs-samtoolsThe last 28 bytes of the BAM file are not equivalent to the standardized 28 byte end-of-file marker.s(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferredt  hs-samtoolsDecode SEQ field to a [Word8] (each byte represents two bases).  hs-samtoolsExtract a sub ByteString starting from and including the first occurrence of the given byte.  hs-samtoolsExtract a sub ByteString up to and including the first occurrence of a given byte. (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< hs-samtoolsDefines a parser for the optional aopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<9 hs-samtoolsDefines a parser for the optional bopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< hs-samtoolsDefines a parser for the optional bigcopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< hs-samtoolsDefines a parser for the optional bigiopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<e hs-samtoolsDefines a parser for the optional bigsopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. (c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< hs-samtoolsDefines a parser for the optional fopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.!(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<' hs-samtoolsDefines a parser for the optional hopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation."(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< hs-samtoolsDefines a parser for the optional smallcopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.#(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< hs-samtoolsDefines a parser for the optional smalliopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.$(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<Y hs-samtoolsDefines a parser for the optional smallsopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.%(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< hs-samtoolsDefines a parser for the optional zopt field of alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.&(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&(7<) hs-samtoolsBAM_V1_6_BAM_Alignment parser.Defines a parser for the alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.'(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred  hs-samtools Define the BAM_V1_6_BAM_BAMAlignments parser.((c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred ^ hs-samtools"BAM_V1_6_BAM_Reference_Information parser.Defines a parser for the alignment section of the BAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.)(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred  hs-samtools Define the BAM_V1_6_BAM_BAMHeader parser.*(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred  hs-samtools Define the  BAM_V1_6_BAM parser.+(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred # hs-samtools)Defines a parser for a single BGZF block.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.,(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred   hs-samtools Define the BAM_V1_6 parser.  hs-samtoolsRun the SAM_V1_6 parser. hs-samtoolsRead a BAM_V1_6 from a file./The file is checked for errors as it is parsed.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsInput path to BAM file.-(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred 7< hs-samtoolsCustom BAM_V1_6- (BAM version 1.6) error data type. See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsNo data to write to file. hs-samtools>HOPT alignment optional field is not hex-formatted byte array.t(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferredp  hs-samtoolsEncode a [Word8] (each byte represents two bases) into a ByteString representing the SEQ field. .(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred   hs-samtoolsDeconstruct a BAM_V1_6 and write to a file. hs-samtoolsWrite a BAM_V1_6 to a file.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsOutput path to BAM file./(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<K hs-samtoolsCustom SAM (version 1.6) SAM_V1_6_Alignment_AOPT data type.See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.0(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7< hs-samtoolscCsSiIf% of the last optional field (type B).See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolscCsSiI&f of the last optional field (type B).See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolscCsSi'If of the last optional field (type B).See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolscCsS(iIf of the last optional field (type B).See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolscCs)SiIf of the last optional field (type B).See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolscC*sSiIf of the last optional field (type B).See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsc+CsSiIf of the last optional field (type B).See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsCustom SAM (version 1.6) &SAM_V1_6_Alignment_OptionalFields_BOPT data type.See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.,,1(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7< hs-samtoolsCustom SAM (version 1.6) &SAM_V1_6_Alignment_OptionalFields_FOPT data type.See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.2(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<D hs-samtoolsCustom SAM (version 1.6) &SAM_V1_6_Alignment_OptionalFields_HOPT data type.See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.3(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7< hs-samtoolsCustom SAM (version 1.6) &SAM_V1_6_Alignment_OptionalFields_IOPT data type.See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.4(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7< hs-samtoolsCustom SAM (version 1.6) &SAM_V1_6_Alignment_OptionalFields_ZOPT data type.See section 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.5(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<= hs-samtoolsCustom SAM (version 1.6) !SAM_V1_6_Alignment_OptionalFields data type.See section 1.4 and 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtools!A - [!-~] - Printable characters. hs-samtools!i - [-+]?[0-9]+ - Signed integer. hs-samtoolsf - [-+]?[0-9]*.?[0-9]+([eE][-+]?[0-9]+)? - Single-precision floating number. hs-samtools0Z - [ !-~]* - Printable string, including space. hs-samtools7H - ([0-9A-F][0-9A-F])* - Byte array in the Hex format. hs-samtoolsB - [cCsSiIf]@(,[-+]?[0-9]*.?[0-9]+([eE][-+]?[0-9]+)?)* - Integer or numeric array.6(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<0  hs-samtoolsCustom SAM (version 1.6) SAM_V1_6_Alignment data type.See section 1.4 and 1.5 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsQuery template NAME. reads/segments having identical QNAME are regarded to come from the same template. A QNAME @*@ indicates the information is unavailable. In a SAM file, a read may occupy multiple alignment lines, when its alignment is chimeric or when multiple mappings are given. hs-samtoolsCombination of bitwise FLAGs. hs-samtoolsReference sequence NAME of the alignment. If @SQ header lines are present, RNAME (if not @*@) must be present in one of the SQ-SN tag. An unmapped segment without coordinate has a @*@ at this field. However, an unmapped segment may also have an ordinary coordinate such that it can be placed at a desired position after sorting. If RNAME is @*@, no assumptions can be made about POS and CIGAR. hs-samtools1-based leftmost mapping POSition of the first CIGAR operation that @consumes@ a reference base. The first base in a reference sequence has coordinate 1. POS is set as 0 for an unmapped read without coordinate. If POS is 0, no assumptions can be made about RNAME and CIGAR. hs-samtoolsMAPping Quality. It equals D10 log10 Pr{mapping position is wrong}, rounded to the nearest integer. A value 255 indicates that the mapping quality is not available. hs-samtools&CIGAR string (set @*@ if unavailable). hs-samtoolsReference sequence name of the primary alignment of the NEXT read in the template. For the last read, the next read is the first read in the template. If @SQ header lines are present, RNEXT (if not @*@ or @=@) must be present in one of the SQ-SN tag. This field is set as @*@ when the information is unavailable, and set as @=@ if RNEXT is identical RNAME. If not @=@ and the next read in the template has one primary mapping (see also bit 0x100 in FLAG), this field is identical to RNAME at the primary line of the next read. If RNEXT is @*@, no assumptions can be made on PNEXT and bit 0x20. hs-samtools1-based Position of the primary alignment of the NEXT read in the template. Set as 0 when the information is unavailable. This field equals POS at the primary line of the next read. If PNEXT is 0, no assumptions can be made on RNEXT and bit 0x20. hs-samtoolssigned observed Template LENgth. For primary reads where the primary alignments of all reads in the template are mapped to the same reference sequence, the absolute value of TLEN equals the distance between the mapped end of the template and the mapped start of the template, inclusively (i.e., end D start + 1). Note that mapped base is defined to be one that aligns to the reference as described by CIGAR, hence excludes soft-clipped bases. The TLEN field is positive for the leftmost segment of the template, negative for the rightmost, and the sign for any middle segment is undefined. If segments cover the same coordinates then the choice of which is leftmost and rightmost is arbitrary, but the two ends must still have differing signs. It is set as 0 for a single-segment template or when the information is unavailable (e.g., when the first or last segment of a multi-segment template is unmapped or when the two are mapped to different reference sequences). hs-samtoolssegment SEQuence. This field can be a @*@ when the sequence is not stored. If not a @*@, the length of the sequence must equal the sum of lengths of MIS=X operations in CIGAR. An @=@ denotes the base is identical to the reference base. No assumptions can be made on the letter cases. hs-samtoolsASCII of base QUALity plus 33 (same as the quality string in the Sanger FASTQ format). A base quality is the phred-scaled base error probability which equals D10 log10 Pr{base is wrong}. This field can be a @*@ when quality is not stored. If not a @*@, SEQ must not be a @*@ and the length of the quality string ought to equal the length of SEQ. hs-samtoolsOptional fields.u(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred 7(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<G hs-samtoolsCustom SAM (version 1.6) SAM_V1_6_One_Line_Comment data type.See section 1.3 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.8(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<ϭ hs-samtools SS tag for SAM_V1_6_File_Level_Metadata. hs-samtools GO tag for SAM_V1_6_File_Level_Metadata. hs-samtools SO tag for SAM_V1_6_File_Level_Metadata. hs-samtools VN tag for SAM_V1_6_File_Level_Metadata. hs-samtoolsCustom SAM (version 1.6) SAM_V1_6_File_Level_Metadata data type.See section 1.3 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.9(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<ҁ hs-samtools VN tag for SAM_V1_6_Program. hs-samtools DS tag for SAM_V1_6_Program. hs-samtools PP tag for SAM_V1_6_Program. hs-samtools CL tag for SAM_V1_6_Program. hs-samtools PN tag for SAM_V1_6_Program. hs-samtools ID tag for SAM_V1_6_Program. hs-samtoolsCustom SAM (version 1.6) SAM_V1_6_Program data type.See section 1.3 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.:(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<Z hs-samtools SM tag for SAM_V1_6_Read_Group. hs-samtools PU tag for SAM_V1_6_Read_Group. hs-samtools PM tag for SAM_V1_6_Read_Group. hs-samtools PL tag for SAM_V1_6_Read_Group. hs-samtools PI tag for SAM_V1_6_Read_Group. hs-samtools PG tag for SAM_V1_6_Read_Group. hs-samtools LB tag for SAM_V1_6_Read_Group. hs-samtools KS tag for SAM_V1_6_Read_Group. hs-samtools FO tag for SAM_V1_6_Read_Group. hs-samtools DT tag for SAM_V1_6_Read_Group. hs-samtools DS tag for SAM_V1_6_Read_Group. hs-samtools CN tag for SAM_V1_6_Read_Group. hs-samtools BC tag for SAM_V1_6_Read_Group. hs-samtools ID tag for SAM_V1_6_Read_Group. hs-samtoolsCustom SAM (version 1.6) SAM_V1_6_Read_Group data type.See section 1.3 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.::;(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<ܜ  hs-samtools UR tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools TP tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools SP tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools M5 tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools DS tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools AS tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools AN tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools AH tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools LN tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtools SN tag for &SAM_V1_6_Reference_Sequence_Dictionary. hs-samtoolsCustom SAM (version 1.6) &SAM_V1_6_Reference_Sequence_Dictionary data type.See section 1.3 of the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.**v(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred ݼ<(c) Matthew Mosior 2023 BSD-stylemattm.github@gmail.comportable Safe-Inferred "7<, hs-samtoolsCustom SAM_V1_6 (SAM version 1.6) data type.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation. hs-samtoolsFile-level metadata. Optional. If present, there must be only one @HD line and it must be the first line of the file.  hs-samtoolsReference sequence dictionary. The order of @SQ lines defines the alignment sorting order. hs-samtools7Read group. Unordered multiple @RG lines are allowed. hs-samtoolsProgram. hs-samtoolsOne-line text comment. Unordered multiple @CO lines are allowed. UTF-8 encoding may be used. hs-samtools7The alignment section (mandatory and optional fields).w(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred   hs-samtools(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<V  hs-samtoolsDefines a parser for the optional aopt field of alignment section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  ?(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the optional bopt field of alignment section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  @(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the optional fopt field of alignment section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  A(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<y  hs-samtoolsDefines a parser for the optional hopt field of alignment section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  B(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the optional iopt field of alignment section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  C(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< ;  hs-samtoolsDefines a parser for the optional zopt field of alignment section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  D(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<   hs-samtoolsSAM_V1_6_Alignment parser.Defines a parser for the alignment section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  E(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<   hs-samtoolsSAM_V1_6_One_Line_Comment parser.Defines a parser for @CO tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  F(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< o  hs-samtoolsDefines a parser for the GO tag of the @HD tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  G(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the SO tag of the @HD tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  H(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<#  hs-samtoolsDefines a parser for the SS tag of the @HD tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  I(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<}  hs-samtoolsDefines a parser for the VN tag of the @HD tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  J(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsSAM_V1_6_File_Level_Metadata parser.Defines a parser for @HD tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  K(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<H  hs-samtoolsDefines a parser for the CL tag of the @PG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  L(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the DS tag of the @PG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  M(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the ID tag of the @PG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  N(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<P  hs-samtoolsDefines a parser for the PN tag of the @PG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  O(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the PP tag of the @PG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  P(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the VN tag of the @PG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  Q(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<g  hs-samtoolsSAM_V1_6_Program parser.Defines a parser for @PG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  R(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the BC tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  S(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<  hs-samtoolsDefines a parser for the CN tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  T(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7< o  hs-samtoolsDefines a parser for the DS tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  U(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<!  hs-samtoolsDefines a parser for the DT tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  V(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<#  hs-samtoolsDefines a parser for the FO tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  W(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<$w  hs-samtoolsDefines a parser for the ID tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  X(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<%  hs-samtoolsDefines a parser for the KS tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  Y(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<''  hs-samtoolsDefines a parser for the LB tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  Z(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<(  hs-samtoolsDefines a parser for the PG tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  [(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<)  hs-samtoolsDefines a parser for the PI tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  \(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<+/  hs-samtoolsDefines a parser for the PL tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  ](c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<,  hs-samtoolsDefines a parser for the PM tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  ^(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<-  hs-samtoolsDefines a parser for the PU tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  _(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7</7  hs-samtoolsDefines a parser for the SM tag of the @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  `(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<0  hs-samtoolsSAM_V1_6_Read_Group parser.Defines a parser for @RG tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  a(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<1  hs-samtoolsDefines a parser for the AH tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  b(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<3Q  hs-samtoolsDefines a parser for the AN tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  c(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<4  hs-samtoolsDefines a parser for the AS tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  d(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<6  hs-samtoolsDefines a parser for the DS tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  e(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<7Y  hs-samtoolsDefines a parser for the LN tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  f(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<8  hs-samtoolsDefines a parser for the M5 tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  g(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<:   hs-samtoolsDefines a parser for the SN tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  h(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<;c  hs-samtoolsDefines a parser for the SP tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  i(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<<  hs-samtoolsDefines a parser for the TP tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  j(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<>  hs-samtoolsDefines a parser for the UR tag of the @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  k(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred"#%&7<?  hs-samtools&SAM_V1_6_Reference_Sequence_Dictionary parser.Defines a parser for @SQ tag section of the SAM v1.6 file format.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  l(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred Ar  hs-samtools Define the SAM_V1_6 parser.  hs-samtoolsRun the SAM_V1_6 parser.  hs-samtoolsRead a SAM_V1_6 from a file./The file is checked for errors as it is parsed.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  hs-samtoolsInput path to SAM file.  m(c) Matthew Mosior 2024 BSD-stylemattm.github@gmail.comportable Safe-Inferred CH  hs-samtoolsDeconstruct a SAM_V1_6 to a  .  hs-samtoolsWrite SAM_V1_6' to a file. Calls deconstructSAM_V1_6.  hs-samtoolsWrite a SAM_V1_6 to a file.See the  -http://samtools.github.io/hts-specs/SAMv1.pdfSAM v1.6 specification documentation.  hs-samtoolsOutput path to SAM file.  xxyz{|}~                                                                           !"#$%&'()*+,------.///////000000000000000000000000000000000000000000000000000000000000000000001111111222222233333334444444555555555556666666666666666677777788888888888888888888888888888888899999999999999999999999999999999999999999999999:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<<<<<<<<<<===================================================================== = = = = = = = = = = = = = = = = = = = > ? @ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z [ \ ] ^ _ ` a b c d e f g h i j k l m  r r r r r r r r r r r r r r r r r r r r r r s s s , , t . w l l m  m 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