/usr/include/ncbi-vdb/simple/sra.hpp is in libncbi-vdb-dev 2.8.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 | /*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _hpp_simple_sra_
#define _hpp_simple_sra_
#include <stdint.h>
#include <string>
#include <vector>
#include <exception>
/* NOTES
01. may need our own String abstraction to represent
pointers into cursor cache rather than copies.
std::string may be too heavyweight, but then
the same problem exists in Java... then again,
maybe it's just that we shouldn't use String for
bases...
*/
extern "C"
{
/*----------------------------------------------------------------------
* forwards and typedefs
*/
struct SRA_Spot;
struct SRA_Object;
struct SRA_Sequence;
struct SRA_Reference;
struct SRA_Alignment;
struct SAM_Flags;
struct SAM_Headers;
struct SAM_Alignment;
}
namespace sra
{
/*----------------------------------------------------------------------
* forwards and typedefs
*/
typedef :: std :: string String;
typedef :: std :: exception Exception;
typedef :: SRA_Spot * SRASpotRef;
typedef :: SRA_Object * SRAObjectRef;
typedef :: SRA_Sequence * SRASequenceRef;
typedef :: SRA_Reference * SRAReferenceRef;
typedef :: SRA_Alignment * SRAAlignmentRef;
typedef :: SAM_Flags * SAMFlagsRef;
typedef :: SAM_Headers * SAMHeadersRef;
typedef :: SAM_Alignment * SAMAlignmentRef;
/*----------------------------------------------------------------------
* SRAException
* all exceptions generated within sra :: simple are subclasses
*/
class SRAException : public :: std :: exception
{
public:
const char * what () const
throw ();
SRAException ()
throw ();
SRAException ( const String & message )
throw ();
SRAException ( const char * fmt, ... )
throw ();
public:
// C++ support
SRAException ( const SRAException & x )
throw ();
SRAException & operator = ( const SRAException & x )
throw ();
virtual ~ SRAException ()
throw ();
private:
String msg;
};
/*----------------------------------------------------------------------
* StringRef
* behaves similarly to a String except that it points to
* data held within a cache whenever possible.
*/
class StringRef
{
public:
const char * data () const
throw ();
size_t length () const
throw ();
String toString () const
throw ( SRAException );
public:
StringRef ( const StringRef & s )
throw ();
StringRef & operator = ( const StringRef & s )
throw ();
virtual ~ StringRef ()
throw ();
private:
const char * str;
size_t len;
// TBD - additional opaque stuff for C object references
};
/*----------------------------------------------------------------------
* SRASequence
* SRASequenceIterator
* a nucleotide sequence
*/
class SRASequence
{
public:
/* name
* returns a textual identifier if available
* or a numeric version otherwise
*/
String name () const
throw ( SRAException );
/* length
* return the number of bases in sequence
*/
uint64_t length () const
throw ( SRAException );
/* bases
* returns bases using IUPAC character representation
*/
String bases () const
throw ( SRAException );
/* isReverse
* true if reverse read
*/
bool isReverse () const
throw ( SRAException );
/* colorSpaceNative
* returns true if the native sequence is in color-space
*/
bool colorSpaceNative () const
throw ( SRAException );
/* hasColorSpace
* returns true if sequence can return color-space
*/
bool hasColorSpace () const
throw ();
/* colorSpaceKey
* returns key ( starting base ) for first read
*/
char colorSpaceKey () const
throw ( SRAException );
/* colorSpace
* returns color-space representation
* NB - may fail on some sequences
*/
String colorSpace () const
throw ( SRAException );
/* qualities
* returns per-base/color phred quality scores
*/
std :: vector < uint8_t > qualities () const
throw ( SRAException );
#if 0
// THESE ARE QUESTIONABLE...
// CONVENIENT PLACES TO ACCUMMULATE CRUFT, BUT
// DO WE WANT TO KEEP DRAGGING IT ALONG? AND
// HOW MUCH FACTORIZATION DO WE WANT IN API?
/* isTechnical
* true if the sequence represents a technical read
*/
bool isTechnical () const
throw ( SRAException );
/* hasPrimaryAlignment
* returns true iff any part of sequence is aligned,
* and the sequence is capable of returning an SRAAlignment
*/
bool hasPrimaryAlignment () const
throw ();
/* primaryAlignment
* if the sequence is aligned and the alignment is available
* assign to an SRAAlignment
*/
SRAAlignmentRef primaryAlignment () const
throw ( SRAException );
#endif
public:
// C++ support
SRASequence & operator = ( SRASequenceRef s )
throw ();
SRASequence ( SRASequenceRef s )
throw ();
SRASequence & operator = ( const SRASequence & s )
throw ( SRAException );
SRASequence ( const SRASequence & s )
throw ( SRAException );
~ SRASequence ()
throw ();
protected:
SRASequenceRef self;
};
class SRASequenceIterator : public SRASequence
{
public:
/* next
* advance to the next sequence
* returns false if no more sequences are available
*/
bool next ()
throw ( SRAException );
public:
// C++ support
SRASequenceIterator ( SRASequenceRef r )
throw ();
SRASequenceIterator & operator = ( const SRASequenceIterator & i )
throw ( SRAException );
SRASequenceIterator ( const SRASequenceIterator & i )
throw ( SRAException );
~ SRASequenceIterator ()
throw ();
private:
SRASequence & operator = ( const SRASequence & s )
throw ( SRAException );
SRASequenceIterator & operator = ( SRASequenceRef s )
throw ();
};
/*----------------------------------------------------------------------
* SRASpot
* SRASpotIterator
* a complete machine read,
* including technical and biological segments
*/
class SRASpot : public SRASequence
{
public:
/* platform
* return platform name as string
*/
String platform () const
throw ( SRAException );
/* spotGroup
* returns a spot group name if known
* returns an empty string otherwise
*/
String spotGroup () const
throw ( SRAException );
/* id
* returns the spot's numeric identifier
*/
int64_t id () const
throw ( SRAException );
/* numReads
* return the number of individual sub-sequences
*/
uint32_t numReads () const
throw ( SRAException );
/* reads
* return all reads - mixed technical and biological
*/
SRASequenceIterator reads () const
throw ( SRAException );
/* numBioReads
* the number of biological reads
*/
uint32_t numBioReads () const
throw ( SRAException );
/* bioReads
* return only biological reads
* if "trimmed" is true, apply quality clipping if indicated
*/
SRASequenceIterator bioReads ( bool trimmed = false ) const
throw ( SRAException );
public:
// C++ support
SRASpot & operator = ( SRASpotRef r )
throw ();
SRASpot ( SRASpotRef r )
throw ();
SRASpot & operator = ( const SRASpot & s )
throw ( SRAException );
SRASpot ( const SRASpot & s )
throw ( SRAException );
~ SRASpot ()
throw ();
protected:
SRASpotRef spot;
};
class SRASpotIterator : public SRASpot
{
public:
/* next
* advance to the next spot
* returns false if no more are available
*/
bool next ()
throw ( SRAException );
SRASpotIterator ( SRASpotRef r )
throw ();
SRASpotIterator & operator = ( const SRASpotIterator & i )
throw ( SRAException );
SRASpotIterator ( const SRASpotIterator & i )
throw ( SRAException );
~ SRASpotIterator ()
throw ();
private:
SRASpot & operator = ( const SRASpot & s )
throw ( SRAException );
SRASpotIterator & operator = ( SRASpotRef r )
throw ();
};
/*----------------------------------------------------------------------
* SRAReference
* SRAReferenceIterator
* a reference sequence
*/
class SRAReference : public SRASequence
{
public:
/* name
* returns a textual identifier if available
* or a numeric version otherwise
*/
String name () const
throw ( SRAException );
/* accession
* TBD - explain
*/
String accession () const
throw ( SRAException );
/* isCircular
*/
bool isCircular () const
throw ( SRAException );
/* baseCount
*/
uint64_t baseCount () const
throw ( SRAException );
/* bases
* returns bases using IUPAC character representation
*
* "first" is a zero-based starting position,
* "length" gives the total number of bases, which will be limited
* to the reference boundaries unless circular
*/
String bases ( uint64_t first, uint64_t length ) const
throw ( SRAException );
public:
// C++ support
SRAReference & operator = ( SRAReferenceRef r )
throw ();
SRAReference ( SRAReferenceRef r )
throw ();
SRAReference & operator = ( const SRAReference & r )
throw ( SRAException );
SRAReference ( const SRAReference & r )
throw ( SRAException );
~ SRAReference ()
throw ();
protected:
SRAReferenceRef self;
};
class SRAReferenceIterator : public SRAReference
{
public:
/* next
* advance to the next reference
* returns false if no more are available
*/
bool next ()
throw ( SRAException );
public:
// C++ support
SRAReferenceIterator ( SRAReferenceRef r )
throw ();
SRAReferenceIterator & operator = ( const SRAReferenceIterator & i )
throw ( SRAException );
SRAReferenceIterator ( const SRAReferenceIterator & i )
throw ( SRAException );
~ SRAReferenceIterator ()
throw ();
private:
SRAReference & operator = ( const SRAReference & r )
throw ( SRAException );
SRAReferenceIterator & operator = ( SRAReferenceRef r )
throw ();
};
/*----------------------------------------------------------------------
* SRAAlignment
* SRAAlignmentIterator
* a relationship between two sequences
*/
class SRAAlignment
{
public:
/* querySequence
* get the query sequence
* this is generally the sequence aligned against the reference
*/
SRASequence querySequence () const
throw ( SRAException );
/* reference
* get the reference sequence
*/
SRAReference reference () const
throw ( SRAException );
/* referenceStart
* returns the alignment's zero-based starting coordinate on reference
*/
uint64_t referenceStart () const
throw ( SRAException );
/* referenceLength
* returns the alignment's projected length upon reference
*/
uint64_t referenceLength () const
throw ( SRAException );
/* mappingQuality
* how closely aligned are the sequences
*/
int64_t mappingQuality () const
throw ( SRAException );
/* hasMate
*/
bool hasMate () const
throw ();
/* mate
* retrieve mate if available
*/
SRAAlignmentRef mate () const
throw ( SRAException );
/* need to tell spot-id and read-idx of sequence
this could be available on the sequence object itself, but isn't.
it's very cheap in our case.
*/
/* OTHER STUFF
read group ( should be modeled? should be from sequence? )
is read paired
is pair proper
is read on negative strand
is ( or is not ) primary alignment
is duplicate
is mate unmapped
is mate on negative strand
mate alignment start
*/
public:
// C++ support
SRAAlignment & operator = ( SRAAlignmentRef a )
throw ();
SRAAlignment ( SRAAlignmentRef a )
throw ();
SRAAlignment & operator = ( const SRAAlignment & a )
throw ( SRAException );
SRAAlignment ( const SRAAlignment & a )
throw ( SRAException );
~ SRAAlignment ()
throw ();
protected:
SRAAlignmentRef self;
};
class SRAAlignmentIterator : public SRAAlignment
{
public:
/* next
* advance to the next alignment
*/
bool next ()
throw ( SRAException );
public:
// C++ support
SRAAlignmentIterator ( SRAAlignmentRef a )
throw ();
SRAAlignmentIterator & operator = ( const SRAAlignmentIterator & i )
throw ( SRAException );
SRAAlignmentIterator ( const SRAAlignmentIterator & i )
throw ( SRAException );
~ SRAAlignmentIterator ()
throw ();
private:
SRAAlignment & operator = ( const SRAAlignment & a )
throw ( SRAException );
SRAAlignmentIterator & operator = ( SRAAlignmentRef a )
throw ();
};
/*----------------------------------------------------------------------
* SRAAlignmentDetail
* gives raw information about relationship between sequences
* from the point of view of the query
*/
class SRAAlignmentDetail
{
public:
/* hasOffset
* a vector of boolean values corresponding to each query base
* "false" means that there is no offset to apply to alignment
* "true" means that there is an offset that must be applied
* to the sequence alignment.
*/
std :: vector < bool > hasOffset () const
throw ( SRAException );
/* offset
* a packed vector of alignment offsets to be applied to the
* query position before handling mismatches ( see documentation ).
* NB - this is a signed quantity and can produce a negative
* alignment coordinate in certain cases.
*/
std :: vector < int32_t > offset () const
throw ( SRAException );
/* hasMismatch
* a vector of boolean values corresponding to each query base
* "false" means that the query sequence matches the reference
* "true" means there is a mismatch, and the actual query base
* may be obtained from the mismatch vector.
*/
std :: vector < bool > hasMismatch () const
throw ( SRAException );
/* mismatch
* a packed vector of query bases that differ from reference
* there is one base for every "true" value in hasMismatch
*/
std :: vector < char > mismatch () const
throw ( SRAException );
// C++ constructor from alignment
SRAAlignmentDetail & operator = ( const SRAAlignment & a )
throw ( SRAException );
SRAAlignmentDetail ( const SRAAlignment & a )
throw ( SRAException );
public:
// C++ support
SRAAlignmentDetail & operator = ( SRAAlignmentRef r )
throw ();
SRAAlignmentDetail ( SRAAlignmentRef r )
throw ();
SRAAlignmentDetail & operator = ( const SRAAlignmentDetail & d )
throw ( SRAException );
SRAAlignmentDetail ( const SRAAlignmentDetail & d )
throw ( SRAException );
~ SRAAlignmentDetail ()
throw ();
private:
SRAAlignmentRef self;
};
/*----------------------------------------------------------------------
* SRAObject
* represents an SRA-capable object
*/
class SRAObject
{
public:
/* constructor
* tries to locate object described by "spec"
* does not fully OPEN object
*/
SRAObject ( const String & spec )
throw ( SRAException );
/* combine constructor
* combines two objects into a single object
*/
SRAObject ( const SRAObject & a, const SRAObject & b )
throw ( SRAException );
/* slice
* create a sub-selection of object
* the sub-selection is based upon reference spec
* and/or coordinates within a reference
*/
SRAObjectRef slice ( const String & referenceSpec ) const
throw ( SRAException );
SRAObjectRef slice ( uint64_t reference_start,
uint64_t reference_length, bool fully_contained ) const
throw ( SRAException );
/* open - IDEMPOTENT
* causes object to create internal resources
*/
void open ()
throw ( SRAException );
/* close
* releases underlying resources
* does NOT delete object
*/
void close ()
throw ();
/* getReferences
* returns an iterator of all references included within the object
*/
SRAReferenceIterator getReferences () const
throw ( SRAException );
/* primaryAlignments
* return an iterator of primary alignments
* ordering is based upon object properties
*/
SRAAlignmentIterator primaryAlignments () const
throw ( SRAException );
SRAAlignmentIterator primaryAlignments ( uint64_t startIdx, uint64_t count ) const
throw ( SRAException );
/* secondaryAlignments
* return an iterator of secondary alignments
* ordering is based upon object properties
*/
SRAAlignmentIterator secondaryAlignments () const
throw ( SRAException );
SRAAlignmentIterator secondaryAlignments ( uint64_t startIdx, uint64_t count ) const
throw ( SRAException );
/* allAlignments
* return an iterator of combined primary and secondary alignments
* ordering is based upon object properties
*/
SRAAlignmentIterator allAlignments () const
throw ( SRAException );
/* alignedSequences
* return an iterator of aligned sequences
* ordering is based upon object properties
*/
SRASequenceIterator alignedSequences () const
throw ( SRAException );
SRASequenceIterator alignedSequences ( uint64_t startIdx, uint64_t count ) const
throw ( SRAException );
/* unalignedSequences
* return an iterator of unaligned sequences
*/
SRASequenceIterator unalignedSequences () const
throw ( SRAException );
SRASequenceIterator unalignedSequences ( uint64_t startIdx, uint64_t count ) const
throw ( SRAException );
/* allSequences
* return an iterator of all sequences
*/
SRASequenceIterator allSequences () const
throw ( SRAException );
/* alignedSpots
* return an iterator of fully or partially aligned spots
*/
SRASpotIterator alignedSpots ( bool partially_aligned ) const
throw ( SRAException );
SRASpotIterator alignedSpots ( uint64_t startIdx, uint64_t count, bool partially_aligned ) const
throw ( SRAException );
/* unalignedSpots
* return an iterator of fully unaligned spots
*/
SRASpotIterator unalignedSpots () const
throw ( SRAException );
SRASpotIterator unalignedSpots ( uint64_t startIdx, uint64_t count ) const
throw ( SRAException );
/* allSpots
* return an iterator of all spots
*/
SRASpotIterator allSpots () const
throw ( SRAException );
SRASpotIterator allSpots ( uint64_t startIdx, uint64_t count ) const
throw ( SRAException );
public:
// C++ support
SRAObject & operator = ( SRAObjectRef o )
throw ();
SRAObject ( SRAObjectRef o )
throw ();
SRAObject & operator = ( const SRAObject & o )
throw ( SRAException );
SRAObject ( const SRAObject & o )
throw ( SRAException );
~ SRAObject ()
throw ();
protected:
SRAObjectRef self;
};
/*----------------------------------------------------------------------
* SAMAlignment
* represents data in a SAM/BAM record
*/
class SAMAlignment
{
public:
/* qName
* query-template name
*/
String qName () const
throw ( SRAException );
/* rName
* reference-sequence name
*/
String rName () const
throw ( SRAException );
/* pos
* 1-based leftmost mapping position
* starting position on reference
*/
uint32_t pos () const
throw ( SRAException );
/* mapQ
* mapping quality
*/
uint8_t mapQ () const
throw ( SRAException );
/* cigar
* cigar-string
* a quasi-run-length-encoded representation of alignment traceback
*/
String cigar () const
throw ( SRAException );
/* rNext
* ref. name of the mate/next segment
*/
String rNext () const
throw ( SRAException );
/* pNext
* ref. position of the mate/next segment
*/
uint32_t pNext () const
throw ( SRAException );
/* tLen
* observed template length
*/
int32_t tLen () const
throw ( SRAException );
/* seq
* IUPAC bases or color-space
*/
String seq () const
throw ( SRAException );
/* qual
* returns per-base/color phred-33 quality scores
* NB - phred-33 is an ASCII encoding using offset of 33
*/
String qual () const
throw ( SRAException );
// conversion from SRA alignment
SAMAlignment & operator = ( const SRAAlignment & a )
throw ();
SAMAlignment ( const SRAAlignment & a )
throw ();
public:
// C++ support
SAMAlignment & operator = ( SAMAlignmentRef r )
throw ();
SAMAlignment ( SAMAlignmentRef r )
throw ();
SAMAlignment & operator = ( const SAMAlignment & a )
throw ( SRAException );
SAMAlignment ( const SAMAlignment & a )
throw ( SRAException );
~ SAMAlignment ()
throw ();
protected:
SAMAlignmentRef self;
};
class SAMAlignmentIterator : public SAMAlignment
{
public:
/* next
* advance to the next alignment
*/
bool next ()
throw ( SRAException );
// conversion from SRA alignment iterator
SAMAlignmentIterator & operator = ( const SRAAlignmentIterator & i )
throw ( SRAException );
SAMAlignmentIterator ( const SRAAlignmentIterator & i )
throw ( SRAException );
public:
// C++ support
SAMAlignmentIterator ( SAMAlignmentRef r )
throw ();
SAMAlignmentIterator & operator = ( const SAMAlignmentIterator & i )
throw ( SRAException );
SAMAlignmentIterator ( const SAMAlignmentIterator & i )
throw ( SRAException );
~ SAMAlignmentIterator ()
throw ();
private:
SAMAlignment & operator = ( const SRAAlignment & a )
throw ();
SAMAlignment & operator = ( const SAMAlignment & a )
throw ();
SAMAlignmentIterator & operator = ( SAMAlignmentRef r )
throw ();
};
/*----------------------------------------------------------------------
* SAMHeaders
* attempts to assemble SAM header information
*/
class SAMHeaders
{
public:
/* toString
* generate headers as a text object
*/
String toString () const
throw ( SRAException );
/* TBD
* list of readgroups
*/
// extraction from an object
SAMHeaders & operator = ( const SRAObject & o )
throw ( SRAException );
SAMHeaders ( const SRAObject & o )
throw ( SRAException );
public:
// C++ support
SAMHeaders & operator = ( const SAMHeaders & h )
throw ();
SAMHeaders ( const SAMHeaders & h )
throw ();
~ SAMHeaders ()
throw ();
private:
SAMHeadersRef self;
};
/*----------------------------------------------------------------------
* SAMFlags
* extract "SAM flags" bits/word from an alignment
*/
class SAMFlags
{
public:
/* multipleSegments ( COSTLY )
* template having multiple segments in sequencing
*/
bool multipleSegments () const
throw ( SRAException );
/* properlyAligned ( VERY EXPENSIVE )
* each segment properly aligned according to the aligner
* all the reads are aligned to the same chromosome
*/
bool properlyAligned () const
throw ( SRAException );
/* unmapped
* segment unmapped
*/
bool unmapped () const
throw ( SRAException );
/* mateUnmapped ( COSTLY )
* next segment in the template unmapped
*/
bool mateUnmapped () const
throw ( SRAException );
/* reverseComp
* SEQ being reverse complemented
*/
bool reverseComp () const
throw ( SRAException );
/* mateReverseComp ( VERY EXPENSIVE )
* SEQ of the next segment in the template being reversed
*/
bool mateReverseComp () const
throw ( SRAException );
/* isFirst
* the first segment in the template
*/
bool isFirst () const
throw ( SRAException );
/* isLast
* the last segment in the template
*/
bool isLast () const
throw ( SRAException );
/* isSecondary
* secondary alignment
*/
bool isSecondary () const
throw ( SRAException );
/* failsQualityControl ( COSTLY )
* not passing quality controls
*/
bool failsQualityControl () const
throw ( SRAException );
/* isDuplicate ( COSTLY )
* PCR or optical duplicate
*/
bool isDuplicate () const
throw ( SRAException );
/* bits ( VERY EXPENSIVE )
* access flags as bit-field
* NB - may incur performance penalty
* unless needing all fields, it may be
* cheaper to access bit-fields individually
*/
uint16_t bits () const
throw ( SRAException );
public:
private:
SAMAlignmentRef self;
};
}
#endif /* _hpp_simple_sra_ */
|