1. A system for identifying a mutation, the system comprising a processor coupled to a tangible memory subsystem storing instructions that when executed by the processor cause the system to:
identify a variant, relative to a reference, in a sequence read from an amplicon; and
discard the identified variant without reporting the identified variant as an identified variant if the identified variant maps to the reference within a recognition site for a primer that created the amplicon.
2. The system of claim 1, further operable to identify a plurality of variants for a plurality of sequence reads from the amplicon.
3. The system of claim 2, further comprising a nucleic acid sequencing instrument, the system further operable to obtain the plurality of sequence reads and group the sequence reads by source amplicons.
4. The system of claim 2, further operable to receive the sequence reads from a nucleic acid sequencing instrument.
5. The system of claim 2, further operable find an alignment between each of the sequence reads and the reference.
6. The system of claim 5, further operable to:
call a plurality of variants relative to the reference; and
provide a report of variants that includes those variants of the plurality of variants that map to the reference outside of a primer recognition site for an amplicon from which the pertinent sequence reads were obtained.
7. The system of claim 6, further operable to exclude from the report those variants of the plurality of variants that map to the reference inside of a primer recognition site for an amplicon from which the pertinent sequence read was obtained.
8. The system of claim 7, wherein the reference comprises a reference directed acyclic graph (DAG), wherein the reference DAG comprises objects in the tangible memory subsystem, wherein segments of known reference sequences that match each other when aligned are each represented by a single object in the reference DAG.
9. The system of claim 8, wherein the system finds the alignments by using the processor to convert each sequence read into the alignment by performing a multi-dimensional look-back operation to find a highest-scoring trace through a multi-dimensional matrix.
10. The system of claim 8, wherein objects in the reference DAG use pointers to adjacent ones of the objects such that the objects are linked into paths to represent the plurality of known sequences, wherein each pointer identifies a physical location in the memory subsystem at which the adjacent object is stored.
11. A method of identifying a mutation, the method comprising:
identifying a variant, relative to a reference, in a sequence read from an amplicon; and
discarding the identified variant without reporting the identified variant as an identified variant if the identified variant maps to the reference within a recognition site for a primer that created the amplicon.
12. The method of claim 11, further comprising identifying a plurality of variants for a plurality of sequence reads from the amplicon.
13. The method of claim 11, further comprising obtaining a plurality of sequence reads and grouping the sequence reads by their source amplicons.
14. The method of claim 13, further comprising obtaining the sequence reads from a sample from a patient.
15. The method of claim 14, further comprising using a computer system comprising a processor coupled to a non-transitory memory to performing the obtaining, identifying, and discarding steps, the method further comprising finding alignments between the plurality of sequence reads and the reference.
16. The method of claim 15, further comprising:
calling a plurality of variants relative to the reference; and
providing a report of variants that includes those variants of the plurality of variants that map to the reference outside of a primer recognition site for an amplicon from which the pertinent sequence reads were obtained.
17. The method of claim 16, wherein the reference comprises a genomic directed acyclic graph (DAG), wherein the reference DAG comprises objects in the tangible memory subsystem, wherein segments of known reference sequences that match each other when aligned are each represented by a single object in the reference DAG.
18. The method of claim 17, further comprising excluding from the report those variants of the plurality of variants that map to the reference inside of a primer recognition site for an amplicon from which the pertinent sequence read was obtained.
19. The method of claim 18, wherein the computer system finds the alignments by using the processor to convert each sequence read into the alignment by performing a multi-dimensional look-back operation to find a highest-scoring trace through a multi-dimensional matrix.
20. The method of claim 19, wherein objects in the reference DAG include pointers to adjacent ones of the objects such that the objects are linked into paths to represent the plurality of known sequences, wherein each pointer identifies a physical location in the memory subsystem at which the adjacent object is stored.
21. The method of claim 19, wherein objects of the reference DAG comprise vertex objects connected by edge objects and an adjacency list for each vertex object and edge object, wherein the adjacency list for a vertex object or edge object lists the edge objects or vertex objects to which that vertex object or edge object is adjacent, wherein each entry in an adjacency list is a pointer to the adjacent vertex object or edge object, wherein each pointer identifies a physical location in the memory subsystem at which the adjacent object is stored.
22. The method of claim 19, wherein the reference DAG uses index-free adjacency to link the objects into paths to represent the plurality of known sequences.
23. A method of identifying a mutation, the method comprising:
aligning sequence reads to a reference;
associating the sequence reads with an amplicon from which the sequence reads were produced;
calling as variants positions in the aligned sequence reads that vary from corresponding positions in the reference; and
discarding called variants that align to the reference within a binding site for a primer used to produce the amplicon.
24. The method of claim 23, wherein the sequence reads are obtained by sequencing nucleic acid from a subject.
25. The method of claim 24, further comprising providing a report of mutations in the subject, wherein each variant:
is called from a set of sequence reads from an associated amplicon produced by an associated primer; and
is included in the report only if that variant aligns to the reference outside of a binding site for the associated primer.
26. The method of claim 25, wherein the reference comprises a genomic DAG stored in a computer system comprising a processor coupled to a non-transitory memory, and further wherein the processor performs the calling, associating, and providing steps.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A macro lens system comprising:
a stop;
a first lens group located in front of the stop, and having a positive refractive power and configured to move during focusing;
a second lens group located behind the stop, and having a positive refractive power;
a 3-1 lens group located behind the second lens group, having a positive refractive power, and configured to move in a direction perpendicular to an optical axis to correct an image blur; and
a 3-2 lens group located behind the 3-1 lens group and having a positive refractive power for correcting a residual aberration,
wherein at least one of the following is configured to change during a focusing operation: a distance between the second lens group and the 3-1 lens group and a distance between the 3-1 lens group and the 3-2 lens group, and the macro lens system satisfies the following equation,
2.5\u2266|\u0394l OBJfOIS|\u226610
where, \u0394IOBJ denotes a distance from a side surface of a lens of the first lens group that is closest to an object, to the object when the lens system is in a maximum magnification of the object position, and fOIS denotes a distance the first lens group is moved during a focusing operation from an infinity focus position to the maximum magnification of the object position, and wherein the term lens group is used to indicate one or more lenses.
2. The macro lens system of claim 1, wherein the first lens group and the second lens group are configured to simultaneously move during focusing, the 3-1 lens group is configured to move during focusing, and the 3-2 lens group is configured not to move during focusing.
3. The macro lens system of claim 1, wherein the first lens group and the second lens group are configured to simultaneously move during focusing, the 3-2 lens group is configured to move during focusing, and the 3-1 lens group does not move during focusing.
4. The macro lens system of claim 1, wherein the first lens group and the second lens group are configured to independently move from each other during focusing, and the 3-1 lens group is configured not to move during focusing.
5. The macro lens system of claim 1, wherein the 3-1 lens group comprises a first lens and a second lens.
6. The macro lens system of claim 5, wherein the first lens has a convex surface toward an image side, and the second lens has a double-concave shape.
7. The macro lens system of claim 5, wherein the first lens and the second lens are cemented to each other in the 3-1 lens group.
8. The macro lens system of claim 1, wherein the 3-2 lens group includes one lens.
9. The macro lens system of claim 1, wherein a maximum magnification of the macro lens system is within a range of \u22120.5 to \u22121.
10. The macro lens system of claim 1, wherein a magnification of the macro lens system is within a range of 0 to \u22121.
11. An image pickup device comprising:
a macro lens system; and
an imaging sensor for receiving an image focused by the macro lens system,
wherein the macro lens system comprises:
a stop;
a first lens group located in front of the stop, and having a positive refractive power and configured to move during focusing;
a second lens group located behind the stop, and having a positive refractive power;
a 3-1 lens group located behind the second lens group, having a positive refractive power, and configured to move in a direction perpendicular to an optical axis to correct an image blur; and
a 3-2 lens group located behind the 3-1 lens group having a positive refractive power for correcting a residual aberration,
wherein at least one of the following is configured to change during a focusing operation: a distance between the second lens group and the 3-1 lens group and a distance between the 3-1 lens group and the 3-2 lens group, and the macro lens system satisfies the following equation,
2.5\u2266|\u0394l OBJfOIS|\u226610
where, \u0394IOBJ denotes a first distance from a side surface of a lens of the first lens group that is closest to an object, to the object when the lens system is in a maximum magnification of the object position, and fOIS denotes a second distance the first lens group is moved during a focusing operation from an infinity focus position to the maximum magnification of the object position, and wherein the term lens group is used to indicate one or more lenses.
12. The image pickup device of claim 11, wherein the first lens group and the second lens group are configured to simultaneously move during focusing, the 3-1 lens group is configured to move during focusing, and the 3-2 lens group is configured to not move during focusing.
13. The image pickup device of claim 11, wherein the first lens group and the second lens group are configured to simultaneously move, the 3-2 lens group is configured to move during focusing, and the 3-1 lens group is configured to not move during focusing.
14. The image pickup device of claim 11, wherein the first lens group and the second lens group are configured to independently move from each other during focusing, and the 3-1 lens group is configured not to move during focusing.
15. The image pickup device of claim 11, wherein the 3-1 lens group comprises a first lens and a second lens.
16. The macro lens system of claim 15, wherein the first lens has a convex surface toward an image side, and the second lens has a double-concave shape.
17. The macro lens system of claim 15, wherein the first lens and the second lens are cemented to each other in the 3-1 lens group.
18. The macro lens system of claim 11, wherein the 3-2 lens group includes one lens.
19. The macro lens system of claim 11, wherein a maximum magnification of the macro lens system is within a range of \u22120.5 to \u22121.
20. The macro lens system of claim 11, wherein a magnification of the macro lens system is within a range of 0 to \u22121.