diff --git a/CHANGELOG.md b/CHANGELOG.md --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -88,3 +88,8 @@ * Adding functionality to write SAM_V1_6(..) to file. * Made show instances of many newtypes/datatypes more verbose to match fields of said newtypes/datatypes. * Added initial writeSAM_V1_6 test case. + +## 0.8.0.1 -- 2023-10-31 + +* Fixed BOPT deconstruction in deconstructSAM_V1_6 (writeSAM_V1_6). +* Added extra writeSAM_V1_6 test cases. diff --git a/hs-samtools.cabal b/hs-samtools.cabal --- a/hs-samtools.cabal +++ b/hs-samtools.cabal @@ -20,7 +20,7 @@ -- PVP summary: +-+------- breaking API changes -- | | +----- non-breaking API additions -- | | | +--- code changes with no API change -version: 0.8.0.0 +version: 0.9.0.0 -- A short (one-line) description of the package. synopsis: Read and write SAM, BAM, and CRAM files. diff --git a/src/Data/SAM/Version1_6/Write/Base.hs b/src/Data/SAM/Version1_6/Write/Base.hs --- a/src/Data/SAM/Version1_6/Write/Base.hs +++ b/src/Data/SAM/Version1_6/Write/Base.hs @@ -33,9 +33,9 @@ import Data.SAM.Version1_6.Alignment.BOPT import Data.ByteString as DB (pack,singleton) +import Data.ByteString.Lazy as DBL (filter) import Data.ByteString.Lazy.Char8 as DBLC8 (fromStrict,unpack) import Data.Foldable (toList) -import Data.Int (Int8,Int16,Int32) import Data.List (intercalate) import Data.Word import Data.ByteString.Builder (toLazyByteString,word16LE,word32LE) @@ -47,7 +47,8 @@ -> String deconstructSAM_V1_6 samv16 = ( intercalate "\n" $ - filter (not . null) [ sam_v1_6_file_level_metadata_tos + Prelude.filter (not . Prelude.null) + [ sam_v1_6_file_level_metadata_tos , sam_v1_6_reference_sequence_dictionary_tos , sam_v1_6_read_group_tos , sam_v1_6_program_tos @@ -87,13 +88,13 @@ sam_v1_6_file_level_metadata_tos = case (sam_v1_6_file_level_metadata samv16) of Nothing -> "" Just hdf -> intercalate "\t" $ - filter (not . null) $ - [ "@HD" - , sam_v1_6_file_level_metadata_format_version_tos hdf - , sam_v1_6_file_level_metadata_sorting_order_tos hdf - , sam_v1_6_file_level_metadata_alignment_grouping_tos hdf - , sam_v1_6_file_level_metadata_subsorting_order_tos hdf - ] + Prelude.filter (not . Prelude.null) $ + [ "@HD" + , sam_v1_6_file_level_metadata_format_version_tos hdf + , sam_v1_6_file_level_metadata_sorting_order_tos hdf + , sam_v1_6_file_level_metadata_alignment_grouping_tos hdf + , sam_v1_6_file_level_metadata_subsorting_order_tos hdf + ] sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tos x = "SN:" ++ ( unpack $ fromStrict $ @@ -166,19 +167,19 @@ Nothing -> "" Just sqf -> intercalate "\n" $ map (\x -> intercalate "\t" $ - filter (not .null) $ - [ "@SQ" - , sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tos x - , sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tos x - , sam_v1_6_reference_sequence_dictionary_alternative_locus_tos x - , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tos x - , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tos x - , sam_v1_6_reference_sequence_dictionary_description_tos x - , sam_v1_6_reference_sequence_dictionary_md5_checksum_tos x - , sam_v1_6_reference_sequence_dictionary_species_tos x - , sam_v1_6_reference_sequence_dictionary_molecule_topology_tos x - , sam_v1_6_reference_sequence_dictionary_uri_tos x - ] + Prelude.filter (not . Prelude.null) $ + [ "@SQ" + , sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tos x + , sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tos x + , sam_v1_6_reference_sequence_dictionary_alternative_locus_tos x + , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names_tos x + , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tos x + , sam_v1_6_reference_sequence_dictionary_description_tos x + , sam_v1_6_reference_sequence_dictionary_md5_checksum_tos x + , sam_v1_6_reference_sequence_dictionary_species_tos x + , sam_v1_6_reference_sequence_dictionary_molecule_topology_tos x + , sam_v1_6_reference_sequence_dictionary_uri_tos x + ] ) (toList sqf) sam_v1_6_read_group_identifer_tos x = "ID:" ++ ( unpack $ @@ -281,23 +282,23 @@ Nothing -> "" Just rgf -> intercalate "\n" $ map (\x -> intercalate "\t" $ - filter (not . null) $ - [ "@RG" - , sam_v1_6_read_group_identifer_tos x - , sam_v1_6_read_group_barcode_sequence_tos x - , sam_v1_6_read_group_sequencing_center_tos x - , sam_v1_6_read_group_description_tos x - , sam_v1_6_read_group_run_date_tos x - , sam_v1_6_read_group_flow_order_tos x - , sam_v1_6_read_group_key_sequence_tos x - , sam_v1_6_read_group_library_tos x - , sam_v1_6_read_group_programs_tos x - , sam_v1_6_read_group_predicted_median_insert_size_tos x - , sam_v1_6_read_group_platform_tos x - , sam_v1_6_read_group_platform_model_tos x - , sam_v1_6_read_group_platform_unit_tos x - , sam_v1_6_read_group_sample_tos x - ] + Prelude.filter (not . Prelude.null) $ + [ "@RG" + , sam_v1_6_read_group_identifer_tos x + , sam_v1_6_read_group_barcode_sequence_tos x + , sam_v1_6_read_group_sequencing_center_tos x + , sam_v1_6_read_group_description_tos x + , sam_v1_6_read_group_run_date_tos x + , sam_v1_6_read_group_flow_order_tos x + , sam_v1_6_read_group_key_sequence_tos x + , sam_v1_6_read_group_library_tos x + , sam_v1_6_read_group_programs_tos x + , sam_v1_6_read_group_predicted_median_insert_size_tos x + , sam_v1_6_read_group_platform_tos x + , sam_v1_6_read_group_platform_model_tos x + , sam_v1_6_read_group_platform_unit_tos x + , sam_v1_6_read_group_sample_tos x + ] ) (toList rgf) sam_v1_6_program_record_identifier_tos x = "ID:" ++ ( unpack $ @@ -343,56 +344,56 @@ sam_v1_6_program_tos = case (sam_v1_6_program samv16) of Nothing -> "" Just pgf -> intercalate "\t" $ - filter (not . null) $ - [ "@PG" - , sam_v1_6_program_record_identifier_tos pgf - , sam_v1_6_program_name_tos pgf - , sam_v1_6_program_command_line_tos pgf - , sam_v1_6_program_previous_pg_id_tos pgf - , sam_v1_6_program_description_tos pgf - , sam_v1_6_program_version_tos pgf - ] + Prelude.filter (not . Prelude.null) $ + [ "@PG" + , sam_v1_6_program_record_identifier_tos pgf + , sam_v1_6_program_name_tos pgf + , sam_v1_6_program_command_line_tos pgf + , sam_v1_6_program_previous_pg_id_tos pgf + , sam_v1_6_program_description_tos pgf + , sam_v1_6_program_version_tos pgf + ] sam_v1_6_one_line_comment_tos = case (sam_v1_6_one_line_comment samv16) of Nothing -> "" Just cof -> intercalate "\n" $ map (\x -> intercalate "\t" $ - filter (not . null) - [ "@CO" - , unpack $ - fromStrict $ - sam_v1_6_one_line_comment_value x - ] + Prelude.filter (not . Prelude.null) + [ "@CO" + , unpack $ + fromStrict $ + sam_v1_6_one_line_comment_value x + ] ) (toList cof) sam_v1_6_alignment_tos = intercalate "\n" $ - map (\x -> case (null $ sam_v1_6_alignment_opts x) of + map (\x -> case (Prelude.null $ sam_v1_6_alignment_opts x) of True -> sam_v1_6_alignment_mand x False -> intercalate "\t" [ sam_v1_6_alignment_mand x , sam_v1_6_alignment_opts x ] ) (toList $ sam_v1_6_alignment samv16) sam_v1_6_alignment_mand x = intercalate "\t" $ - filter (not . null) - [ unpack $ fromStrict $ sam_v1_6_alignment_qname x - , show $ sam_v1_6_alignment_flag x - , unpack $ fromStrict $ sam_v1_6_alignment_rname x - , show $ sam_v1_6_alignment_pos x - , show $ sam_v1_6_alignment_mapq x - , unpack $ fromStrict $ sam_v1_6_alignment_cigar x - , unpack $ fromStrict $ sam_v1_6_alignment_rnext x - , show $ sam_v1_6_alignment_pnext x - , show $ sam_v1_6_alignment_tlen x - , unpack $ fromStrict $ sam_v1_6_alignment_seq x - , unpack $ fromStrict $ sam_v1_6_alignment_qual x - ] + Prelude.filter (not . Prelude.null) + [ unpack $ fromStrict $ sam_v1_6_alignment_qname x + , show $ sam_v1_6_alignment_flag x + , unpack $ fromStrict $ sam_v1_6_alignment_rname x + , show $ sam_v1_6_alignment_pos x + , show $ sam_v1_6_alignment_mapq x + , unpack $ fromStrict $ sam_v1_6_alignment_cigar x + , unpack $ fromStrict $ sam_v1_6_alignment_rnext x + , show $ sam_v1_6_alignment_pnext x + , show $ sam_v1_6_alignment_tlen x + , unpack $ fromStrict $ sam_v1_6_alignment_seq x + , unpack $ fromStrict $ sam_v1_6_alignment_qual x + ] sam_v1_6_alignment_opts x = intercalate "\t" $ - filter (not . null) - [ sam_v1_6_alignment_aopt_d x - , sam_v1_6_alignment_iopt_d x - , sam_v1_6_alignment_fopt_d x - , sam_v1_6_alignment_zopt_d x - , sam_v1_6_alignment_hopt_d x - , sam_v1_6_alignment_bopt_d x - ] + Prelude.filter (not . Prelude.null) + [ sam_v1_6_alignment_aopt_d x + , sam_v1_6_alignment_iopt_d x + , sam_v1_6_alignment_fopt_d x + , sam_v1_6_alignment_zopt_d x + , sam_v1_6_alignment_hopt_d x + , sam_v1_6_alignment_bopt_d x + ] sam_v1_6_alignment_aopt_d x = case (sam_v1_6_alignment_aopt x) of Nothing -> "" Just aopt -> ( unpack $ @@ -459,74 +460,82 @@ sam_v1_6_alignment_bopt_d x = case (sam_v1_6_alignment_bopt x) of Nothing -> "" Just bopt -> concat $ - filter (not . null) - [ sam_v1_6_alignment_bopt_int8_d bopt - , sam_v1_6_alignment_bopt_word8_d bopt - , sam_v1_6_alignment_bopt_int16_d bopt - , sam_v1_6_alignment_bopt_word16_d bopt - , sam_v1_6_alignment_bopt_int32_d bopt - , sam_v1_6_alignment_bopt_word32_d bopt - , sam_v1_6_alignment_bopt_float_d bopt - ] + Prelude.filter (not . Prelude.null) + [ sam_v1_6_alignment_bopt_int8_d bopt + , sam_v1_6_alignment_bopt_word8_d bopt + , sam_v1_6_alignment_bopt_int16_d bopt + , sam_v1_6_alignment_bopt_word16_d bopt + , sam_v1_6_alignment_bopt_int32_d bopt + , sam_v1_6_alignment_bopt_word32_d bopt + , sam_v1_6_alignment_bopt_float_d bopt + ] sam_v1_6_alignment_bopt_int8_d x = case (sam_v1_6_alignment_bopt_int8 x) of Nothing -> "" Just bopt_int8 -> (unpack $ fromStrict $ pack $ toList $ sam_v1_6_alignment_bopt_int8_tag bopt_int8) ++ ":" ++ - (unpack $ fromStrict $ singleton $ sam_v1_6_alignment_bopt_int8_type bopt_int8) ++ + "B" ++ ":" ++ - (concat $ map encodeInt8 $ toList $ sam_v1_6_alignment_bopt_int8_value bopt_int8) + (unpack $ fromStrict $ DB.singleton $ sam_v1_6_alignment_bopt_int8_type bopt_int8) ++ + "," ++ + (concat $ map show $ toList $ sam_v1_6_alignment_bopt_int8_value bopt_int8) sam_v1_6_alignment_bopt_word8_d x = case (sam_v1_6_alignment_bopt_word8 x) of Nothing -> "" Just bopt_word8 -> (unpack $ fromStrict $ pack $ toList $ sam_v1_6_alignment_bopt_word8_tag bopt_word8) ++ ":" ++ - (unpack $ fromStrict $ singleton $ sam_v1_6_alignment_bopt_word8_type bopt_word8) ++ + "B" ++ ":" ++ + (unpack $ fromStrict $ DB.singleton $ sam_v1_6_alignment_bopt_word8_type bopt_word8) ++ + "," ++ (unpack $ fromStrict $ pack $ toList $ sam_v1_6_alignment_bopt_word8_value bopt_word8) sam_v1_6_alignment_bopt_int16_d x = case (sam_v1_6_alignment_bopt_int16 x) of Nothing -> "" Just bopt_int16 -> (unpack $ fromStrict $ pack $ toList $ sam_v1_6_alignment_bopt_int16_tag bopt_int16) ++ ":" ++ - (unpack $ fromStrict $ singleton $ sam_v1_6_alignment_bopt_int16_type bopt_int16) ++ + "B" ++ ":" ++ - (concat $ map encodeInt16 $ toList $ sam_v1_6_alignment_bopt_int16_value bopt_int16) + (unpack $ fromStrict $ DB.singleton $ sam_v1_6_alignment_bopt_int16_type bopt_int16) ++ + "," ++ + (concat $ map show $ toList $ sam_v1_6_alignment_bopt_int16_value bopt_int16) sam_v1_6_alignment_bopt_word16_d x = case (sam_v1_6_alignment_bopt_word16 x) of Nothing -> "" Just bopt_word16 -> (unpack $ fromStrict $ pack $ toList $ sam_v1_6_alignment_bopt_word16_tag bopt_word16) ++ ":" ++ - (unpack $ fromStrict $ singleton $ sam_v1_6_alignment_bopt_word16_type bopt_word16) ++ + "B" ++ ":" ++ + (unpack $ fromStrict $ DB.singleton $ sam_v1_6_alignment_bopt_word16_type bopt_word16) ++ + "," ++ (concat $ map encodeWord16 $ toList $ sam_v1_6_alignment_bopt_word16_value bopt_word16) sam_v1_6_alignment_bopt_int32_d x = case (sam_v1_6_alignment_bopt_int32 x) of Nothing -> "" Just bopt_int32 -> (unpack $ fromStrict $ pack $ toList $ sam_v1_6_alignment_bopt_int32_tag bopt_int32) ++ ":" ++ - (unpack $ fromStrict $ singleton $ sam_v1_6_alignment_bopt_int32_type bopt_int32) ++ + "B" ++ ":" ++ - (concat $ map encodeInt32 $ toList $ sam_v1_6_alignment_bopt_int32_value bopt_int32) + (unpack $ fromStrict $ DB.singleton $ sam_v1_6_alignment_bopt_int32_type bopt_int32) ++ + "," ++ + (concat $ map show $ toList $ sam_v1_6_alignment_bopt_int32_value bopt_int32) sam_v1_6_alignment_bopt_word32_d x = case (sam_v1_6_alignment_bopt_word32 x) of Nothing -> "" Just bopt_word32 -> (unpack $ fromStrict $ pack $ toList $ sam_v1_6_alignment_bopt_word32_tag bopt_word32) ++ ":" ++ - (unpack $ fromStrict $ singleton $ sam_v1_6_alignment_bopt_word32_type bopt_word32) ++ + "B" ++ ":" ++ + (unpack $ fromStrict $ DB.singleton $ sam_v1_6_alignment_bopt_word32_type bopt_word32) ++ + "," ++ (concat $ map encodeWord32 $ toList $ sam_v1_6_alignment_bopt_word32_value bopt_word32) sam_v1_6_alignment_bopt_float_d x = case (sam_v1_6_alignment_bopt_float x) of Nothing -> "" Just bopt_float -> (unpack $ fromStrict $ pack $ toList $ sam_v1_6_alignment_bopt_float_tag bopt_float) ++ ":" ++ - (unpack $ fromStrict $ singleton $ sam_v1_6_alignment_bopt_float_type bopt_float) ++ + "B" ++ ":" ++ + (unpack $ fromStrict $ DB.singleton $ sam_v1_6_alignment_bopt_float_type bopt_float) ++ + "," ++ (concat $ map show $ toList $ sam_v1_6_alignment_bopt_float_value bopt_float) - encodeInt8 :: Int8 -> [Char] - encodeInt8 = show - encodeInt16 :: Int16 -> [Char] - encodeInt16 = show encodeWord16 :: Word16 -> [Char] - encodeWord16 = unpack . toLazyByteString . word16LE - encodeInt32 :: Int32 -> [Char] - encodeInt32 = show + encodeWord16 = unpack . DBL.filter (\x -> x /= 0) . toLazyByteString . word16LE encodeWord32 :: Word32 -> [Char] - encodeWord32 = unpack . toLazyByteString . word32LE + encodeWord32 = unpack . DBL.filter (\x -> x /= 0) . toLazyByteString . word32LE -- | Write @"SAM_V1_6"@ to a file. -- Calls deconstructSAM_V1_6. diff --git a/test/Main.hs b/test/Main.hs --- a/test/Main.hs +++ b/test/Main.hs @@ -31,12 +31,30 @@ readSAM_V1_6 "test/examples/toy1.sam" `shouldReturn` toy1sam describe "Data.SAM.Version1_6.Write.Base" $ do describe "writeSAM_V1_6" $ do + describe "toy5.sam" $ do + it "Ensures writeSAM_V1_6 produces the a sam file equivalent to what was parsed via readSAM_V1_6." $ do + toy5 <- readSAM_V1_6 "test/examples/toy5.sam" + writeSAM_V1_6 "test/examples/toy5f.sam" toy5 + toy5f <- readSAM_V1_6 "test/examples/toy5f.sam" + toy5 `shouldBe` toy5f + describe "toy4.sam" $ do + it "Ensures writeSAM_V1_6 produces the a sam file equivalent to what was parsed via readSAM_V1_6." $ do + toy4 <- readSAM_V1_6 "test/examples/toy4.sam" + writeSAM_V1_6 "test/examples/toy4f.sam" toy4 + toy4f <- readSAM_V1_6 "test/examples/toy4f.sam" + toy4 `shouldBe` toy4f describe "toy2.sam" $ do it "Ensures writeSAM_V1_6 produces the a sam file equivalent to what was parsed via readSAM_V1_6." $ do toy2 <- readSAM_V1_6 "test/examples/toy2.sam" writeSAM_V1_6 "test/examples/toy2f.sam" toy2 toy2f <- readSAM_V1_6 "test/examples/toy2f.sam" - toy2 `shouldBe` toy2f + toy2 `shouldBe` toy2f + describe "toy1.sam" $ do + it "Ensures writeSAM_V1_6 produces the a sam file equivalent to what was parsed via readSAM_V1_6." $ do + toy1 <- readSAM_V1_6 "test/examples/toy1.sam" + writeSAM_V1_6 "test/examples/toy1f.sam" toy1 + toy1f <- readSAM_V1_6 "test/examples/toy1f.sam" + toy1 `shouldBe` toy1f where toy1sam = SAM_V1_6 { sam_v1_6_file_level_metadata = Nothing , sam_v1_6_reference_sequence_dictionary = Just (fromList [SAM_V1_6_Reference_Sequence_Dictionary { sam_v1_6_reference_sequence_dictionary_reference_sequence_name = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value = fromString "ref" } , sam_v1_6_reference_sequence_dictionary_reference_sequence_length = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value = fromString "45" } , sam_v1_6_reference_sequence_dictionary_alternative_locus = Nothing , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names = Nothing , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier = Nothing , sam_v1_6_reference_sequence_dictionary_description = Nothing , sam_v1_6_reference_sequence_dictionary_md5_checksum = Nothing , sam_v1_6_reference_sequence_dictionary_species = Nothing , sam_v1_6_reference_sequence_dictionary_molecule_topology = Nothing , sam_v1_6_reference_sequence_dictionary_uri = Nothing },SAM_V1_6_Reference_Sequence_Dictionary { sam_v1_6_reference_sequence_dictionary_reference_sequence_name = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value = fromString "ref2" } , sam_v1_6_reference_sequence_dictionary_reference_sequence_length = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value = fromString "40" } , sam_v1_6_reference_sequence_dictionary_alternative_locus = Nothing , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names = Nothing , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier = Nothing , sam_v1_6_reference_sequence_dictionary_description = Nothing , sam_v1_6_reference_sequence_dictionary_md5_checksum = Nothing , sam_v1_6_reference_sequence_dictionary_species = Nothing , sam_v1_6_reference_sequence_dictionary_molecule_topology = Nothing , sam_v1_6_reference_sequence_dictionary_uri = Nothing }]) , sam_v1_6_read_group = Nothing , sam_v1_6_program = Nothing , sam_v1_6_one_line_comment = Nothing , sam_v1_6_alignment = fromList [SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r001" , sam_v1_6_alignment_flag = 163 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 7 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "8M4I4M1D3M" , sam_v1_6_alignment_rnext = fromString "=" , sam_v1_6_alignment_pnext = 37 , sam_v1_6_alignment_tlen = 39 , sam_v1_6_alignment_seq = fromString "TTAGATAAAGAGGATACTG" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Just SAM_V1_6_Alignment_BOPT { sam_v1_6_alignment_bopt_int8 = Nothing , sam_v1_6_alignment_bopt_word8 = Nothing , sam_v1_6_alignment_bopt_int16 = Nothing , sam_v1_6_alignment_bopt_word16 = Just SAM_V1_6_Alignment_BOPT_Word16 { sam_v1_6_alignment_bopt_word16_tag = fromList [88,88] , sam_v1_6_alignment_bopt_word16_type = 83 , sam_v1_6_alignment_bopt_word16_value = fromList [49,50,53,54,49,44,50,44,50,48,44,49,49,50] } , sam_v1_6_alignment_bopt_int32 = Nothing , sam_v1_6_alignment_bopt_word32 = Nothing , sam_v1_6_alignment_bopt_float = Nothing } },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r002" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 9 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "1S2I6M1P1I1P1I4M2I" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "AAAAGATAAGGGATAAA" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r003" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 9 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "5H6M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "AGCTAA" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r004" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 16 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "6M14N1I5M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "ATAGCTCTCAGC" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r003" , sam_v1_6_alignment_flag = 16 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 29 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "6H5M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "TAGGC" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r001" , sam_v1_6_alignment_flag = 83 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 37 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "9M" , sam_v1_6_alignment_rnext = fromString "=" , sam_v1_6_alignment_pnext = 7 , sam_v1_6_alignment_tlen = -39 , sam_v1_6_alignment_seq = fromString "CAGCGCCAT" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "x1" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref2" , sam_v1_6_alignment_pos = 1 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "20M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "aggttttataaaacaaataa" , sam_v1_6_alignment_qual = fromString "????????????????????" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "x2" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref2" , sam_v1_6_alignment_pos = 2 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "21M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "ggttttataaaacaaataatt" , sam_v1_6_alignment_qual = fromString "?????????????????????" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "x3" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref2" , sam_v1_6_alignment_pos = 6 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "9M4I13M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "ttataaaacAAATaattaagtctaca" , sam_v1_6_alignment_qual = fromString "??????????????????????????" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "x4" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref2" , sam_v1_6_alignment_pos = 10 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "25M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "CaaaTaattaagtctacagagcaac" , sam_v1_6_alignment_qual = fromString "?????????????????????????" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "x5" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref2" , sam_v1_6_alignment_pos = 12 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "24M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "aaTaattaagtctacagagcaact" , sam_v1_6_alignment_qual = fromString "????????????????????????" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "x6" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref2" , sam_v1_6_alignment_pos = 14 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "23M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "Taattaagtctacagagcaacta" , sam_v1_6_alignment_qual = fromString "???????????????????????" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing }] } toy2sam = SAM_V1_6 { sam_v1_6_file_level_metadata = Just SAM_V1_6_File_Level_Metadata { sam_v1_6_file_level_metadata_format_version = SAM_V1_6_File_Level_Metadata_Format_Version { sam_v1_6_file_level_metadata_format_version_value = fromString "1.6" } , sam_v1_6_file_level_metadata_sorting_order = Just SAM_V1_6_File_Level_Metadata_Sorting_Order { sam_v1_6_file_level_metadata_sorting_order_value = fromString "coordinate" } , sam_v1_6_file_level_metadata_alignment_grouping = Nothing , sam_v1_6_file_level_metadata_subsorting_order = Nothing } , sam_v1_6_reference_sequence_dictionary = Just (fromList [SAM_V1_6_Reference_Sequence_Dictionary { sam_v1_6_reference_sequence_dictionary_reference_sequence_name = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name { sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value = fromString "ref" } , sam_v1_6_reference_sequence_dictionary_reference_sequence_length = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length { sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value = fromString "45" } , sam_v1_6_reference_sequence_dictionary_alternative_locus = Nothing , sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names = Nothing , sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier = Nothing , sam_v1_6_reference_sequence_dictionary_description = Nothing , sam_v1_6_reference_sequence_dictionary_md5_checksum = Nothing , sam_v1_6_reference_sequence_dictionary_species = Nothing , sam_v1_6_reference_sequence_dictionary_molecule_topology = Nothing , sam_v1_6_reference_sequence_dictionary_uri = Nothing }]) , sam_v1_6_read_group = Nothing , sam_v1_6_program = Nothing , sam_v1_6_one_line_comment = Nothing , sam_v1_6_alignment = fromList [SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r001" , sam_v1_6_alignment_flag = 99 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 7 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "8M2I4M1D3M" , sam_v1_6_alignment_rnext = fromString "=" , sam_v1_6_alignment_pnext = 37 , sam_v1_6_alignment_tlen = 39 , sam_v1_6_alignment_seq = fromString "TTAGATAAAGGATACTG" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r002" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 9 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "3S6M1P1I4M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "AAAAGATAAGGATA" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r003" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 9 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "5S6M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "GCCTAAGCTAA" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Just SAM_V1_6_Alignment_ZOPT { sam_v1_6_alignment_zopt_tag = fromString "SA" , sam_v1_6_alignment_zopt_value = fromString "ref,29,-,6H5M,17,0;" } , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r004" , sam_v1_6_alignment_flag = 0 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 16 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "6M14N5M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "ATAGCTTCAGC" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r003" , sam_v1_6_alignment_flag = 2064 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 29 , sam_v1_6_alignment_mapq = 17 , sam_v1_6_alignment_cigar = fromString "6H5M" , sam_v1_6_alignment_rnext = fromString "*" , sam_v1_6_alignment_pnext = 0 , sam_v1_6_alignment_tlen = 0 , sam_v1_6_alignment_seq = fromString "TAGGC" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Nothing , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Just SAM_V1_6_Alignment_ZOPT { sam_v1_6_alignment_zopt_tag = fromString "SA" , sam_v1_6_alignment_zopt_value = fromString "ref,9,+,5S6M,30,1;" } , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing },SAM_V1_6_Alignment { sam_v1_6_alignment_qname = fromString "r001" , sam_v1_6_alignment_flag = 147 , sam_v1_6_alignment_rname = fromString "ref" , sam_v1_6_alignment_pos = 37 , sam_v1_6_alignment_mapq = 30 , sam_v1_6_alignment_cigar = fromString "9M" , sam_v1_6_alignment_rnext = fromString "=" , sam_v1_6_alignment_pnext = 7 , sam_v1_6_alignment_tlen = -39 , sam_v1_6_alignment_seq = fromString "CAGCGGCAT" , sam_v1_6_alignment_qual = fromString "*" , sam_v1_6_alignment_aopt = Nothing , sam_v1_6_alignment_iopt = Just SAM_V1_6_Alignment_IOPT { sam_v1_6_alignment_iopt_tag = fromString "NM" , sam_v1_6_alignment_iopt_value = 1 } , sam_v1_6_alignment_fopt = Nothing , sam_v1_6_alignment_zopt = Nothing , sam_v1_6_alignment_hopt = Nothing , sam_v1_6_alignment_bopt = Nothing }] }