target padding during alignment #303

ekg · 2024-12-09T21:40:30Z

MashMap doesn't give us precise starts and ends to our mapping. But, we should be able to expand the target region and align the entire query against it to correct for small positional errors. This sets our target-padding -E as 100bp by default.

…rd parsing

…rocess

…d of left

…nction

…ustments

…ctly

…perations

…utput

…tion

…t function

…validation

…t function

…fication

…essing

…tions

…rocess

…uence matching checks

…mparisons

…king

ekg added 30 commits December 2, 2024 16:47

feat: Add target padding option for sequence alignment

7c95af9

refactor: Add target padding with bounds checking during mapping reco…

5a3ce52

…rd parsing

refactor: Remove target_padding from sequence record padding calculation

d34c936

fix: Modify parseMashmapRow to accept target_padding as parameter

abb0680

fix: Update parseMashmapRow call with target_padding parameter

971171a

feat: Adjust CIGAR string based on sequence comparison in alignment p…

de792e5

…rocess

feat: Add logging for original CIGAR string before adjustment

c2176c9

fix: Adjust end deletions in adjust_cigar_string to move right instea…

ae47ec3

…d of left

fix: Adjust left-shifting of initial deletions in CIGAR string alignment

5ee30f3

fix: Declare variable 'idx' before using it in adjust_cigar_string fu…

40dba24

…nction

fix: Correct match representation in CIGAR string after alignment adj…

9699528

…ustments

feat: Implement adjust_cigar_string function to shift deletions corre…

6f27a4c

…ctly

refactor: Optimize CIGAR string adjustment by directly manipulating o…

497f053

…perations

fix: Correct deletion adjustment in CIGAR string processing function

3e16bb2

feat: Update adjust_cigar_string to merge successive CIGAR operations

1f6a0b1

feat: Add functions to trim CIGAR string and recompute identity metrics

172c5ae

fix: Adjust CIGAR string and positions in alignment output processing

ae09e84

fix: Replace identity metrics tags and correct scaling in alignment o…

89cbd15

…utput

chore: Remove debugging output from processAlignment function

550ece5

fix: Prevent extra newline in updated_output in processAlignment func…

6f74c4f

…tion

feat: Set default target_padding to 100bp and update help message

3621ab9

feat: Add CIGAR alignment verification to catch mismatches early

d66f5a3

fix: Handle sequence boundary conditions in alignment processing

9f30629

feat: Add debugging print statements to processAlignment function

b1a98fa

feat: Add debug output for alignment modifications in processAlignmen…

23ea217

…t function

feat: Add detailed debugging output for mismatch errors in alignment …

c192069

…validation

fix: Resolve type mismatch in std::min calls in verify_cigar_alignmen…

294da08

…t function

fix: Update position adjustments in CIGAR trimming and alignment veri…

28bfb43

…fication

feat: Add debug statements to trace CIGAR trimming and alignment proc…

0750fe0

…essing

feat: Validate sequence matches before adjusting CIGAR string operations

319a439

ekg added 30 commits December 12, 2024 13:18

feat: Add function to trim leading/trailing deletions from CIGAR string

daeb8d2

feat: Add debugging messages to track alignment validation steps

e7d5e37

almost there

0dd86ec

correctness

6581d8b

refactor: Remove debugging statements while preserving validity checks

bc8a424

refactor: Remove extra blank line in CIGAR string extraction

e717481

refactor: Remove debug print statement for CIGAR string

e2e70ed

remove double adjustment

05ecbe7

refactor: Optimize CIGAR string merging with more efficient parsing

db72d0d

refactor: Optimize CIGAR string parsing in trim_leading_trailing_dele…

6b9211f

…tions

refactor: Add macro to control CIGAR validation checks

32a0025

feat: Enable CIGAR validation checks by setting VALIDATE_CIGAR to 1

70a06bf

feat: Add detailed debug logging for CIGAR validation and alignment p…

f09a8d0

…rocess

feat: Add CIGAR validation after adjust_cigar_string

d56dba0

feat: Add debug output for alignment record details in worker thread

acd89e2

refactor: Enhance CIGAR string swap validation with comprehensive seq…

4729d7b

…uence matching checks

feat: Add detailed debugging for CIGAR string adjustment character co…

69f9d3d

…mparisons

fix: Correct position calculation in leading deletion swap validation

7d70751

fix: Remove duplicate variable declarations in adjust_cigar_string

ec0c03e

refactor: Add detailed debug logging for CIGAR alignment verification

b0b8d55

fix: Improve CIGAR alignment verification with detailed position trac…

c38e336

…king

fix: Improve CIGAR alignment verification with better position tracking

8424775

fix: Cast int64_t to size_t in std::min calls to resolve type mismatch

2575367

fix: Correct CIGAR string handling for leading mismatched operations

58ebce5

refactor: Simplify CIGAR validation and error reporting

2393761

refactor: Remove debug output for character comparison in alignment

19ea0b2

refactor: Remove debug logging from alignment processing

26b65b9

refactor: Remove debug logging from CIGAR alignment verification

6650676

style: Comment out debug messages in adjust_cigar_string function

31031cd

chore: Comment out debug messages in adjust_cigar_string function

3778769

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

target padding during alignment #303

target padding during alignment #303

ekg commented Dec 9, 2024

target padding during alignment #303

Are you sure you want to change the base?

target padding during alignment #303

Conversation

ekg commented Dec 9, 2024