Several major updates #78

andrewdavidsmith · 2024-10-20T04:27:22Z

Changes include updating submodules. Separating code for each command. Fixing many issues in the code. Adding the functionality to deal with BAM input directly, which now includes the gc_extrap command and threads.

… file

…ence and moved the code dealing with htslib stuff down to the bottom of the source file

…s_MR function

…nctions

…ecord_utils.hcpp as new dependent files

…ts from BAM files for paired-end. This involves using both the tid and pos of the given read along with the tid and pos of its mate. Currently the functionality to return the values of the number of paired reads and the number of reads with mates are not active

…ng bamxx and assuming that mates are identified using the mtid and mpos values within the BAM record

…ds it

…counts for BAM input, which doesn't care about mate pairs

…her, and eliminated a bunch of redundant code

… format

… reads to an outer scope and adding a forgotten section of code to take care of the rest of the priority queue on sorted parts after having examined all reads in a BAM file when estimating coverage

…read is mapped -- the condition was inverted

…for mapped reads

…er of reads in BAM format

…o a file if selected on cli

…f genomic intervals from BAM records

…sorting in the wrong direction

…t eliminating a memory leak that turned out not to exist anyway

…ith the no args help

… has now been included in gc_extrap with BAM input

…onst to args for LU_determinant

…although it was used in a condition and set both true and false in different places, when it was set to false a return always happened immediately

… was never used

…f verbose printing into a function from bound_pop

…comparison

…failing to throw an exception that was constructed

… in initializing the mt19937 which was generating randoms

andrewdavidsmith added 30 commits October 17, 2024 19:21

src/smithlab_cpp: updating submodules

b88ab25

Fixing hashes on test outputs and fixing script for testing lc_extrap

e714421

src/moment_sequence.hcpp: removing unused verbose arguments to functions

300ca41

src/c_curve.cpp: removed code that was not used for c_curve from this…

75a7a5e

… file

src/load_data_for_complexity.hcpp: made filenames pass by const refer…

dba838d

…ence and moved the code dealing with htslib stuff down to the bottom of the source file

src/lc_extrap.cpp: removing c_str

744b7cb

src/gc_extrap.cpp: removing unused verbose arg to load_coverage_count…

ef0f47e

…s_MR function

src/bound_pop.cpp: removing unused verbose arg to quadrature rules fu…

a04135f

…nctions

src/bamxx: Adding bamxx submodule

dc9d4f8

Makefile.am: removing the to-mr target and adding bamxx and src/bam_r…

cc115f6

…ecord_utils.hcpp as new dependent files

Adding back functionality to work with BAM in paired-end mode now usi…

118a092

…ng bamxx and assuming that mates are identified using the mtid and mpos values within the BAM record

src/common.hcpp: adding these files

a0bc9b3

src/bam_record_utils.hcpp: adding these source file

5c1483a

src/dnmt_error.hpp: adding this file because bam_record_utils.cpp nee…

b6aaa24

…ds it

Formatting with clang-format and linting with cpplint

d3454eb

src/load_data_for_complexity.hpp: adding a function to load coverage …

05c2081

…counts for BAM input, which doesn't care about mate pairs

src/load_data_for_complexity.cpp: adding structs to gather data toget…

90148c2

…her, and eliminated a bunch of redundant code

src/gc_extrap.cpp: added functionality to do genome coverage from BAM…

47cd233

… format

Adding threads for functions that read BAM input

3245e62

src/load_data_for_complexity.cpp: factoring out sorted order check on…

c72b53f

… reads to an outer scope and adding a forgotten section of code to take care of the rest of the priority queue on sorted parts after having examined all reads in a BAM file when estimating coverage

src/load_data_for_complexity.cpp: linting with cpplint

0a94079

src/load_data_for_complexity.cpp: fixing a bug in checking whether a …

251d39f

…read is mapped -- the condition was inverted

src/load_data_for_complexity.cpp: another bugfix related to checking …

2b21984

…for mapped reads

src/load_data_for_complexity.cpp: fixing a bug in checking sorted ord…

6562e4a

…er of reads in BAM format

src/smithlab_cpp: updating submodule

7b38e63

src/load_data_for_complexity.cpp: formatting and comments

335ecc9

src/lc_extrap.cpp: adding code to format the histogram and write it t…

197c9e5

…o a file if selected on cli

src/common.hpp: adding the report_histogram to the common sources

c063d4a

src/load_data_for_complexity.cpp: fixing a bug in setting endpoints o…

8cc2b43

…f genomic intervals from BAM records

andrewdavidsmith added 28 commits October 19, 2024 15:01

src/c_curve.cpp: adding the ability to output the counts histogram

87082db

src/gc_extrap.cpp: adding the ability to output the counts histogram

ce52e2b

src/lc_extrap.cpp: moving the report_histogram function to common

99edc6b

src/load_data_for_complexity.cpp: fixed the priority queue which was …

094584a

…sorting in the wrong direction

src/load_data_for_complexity.cpp: removing some code that was aimed a…

d15c897

…t eliminating a memory leak that turned out not to exist anyway

src/lc_extrap.cpp: merging option to report the 'about' information w…

8598eaf

…ith the no args help

src/gc_extrap.cpp: merging option to report the 'about' information w…

4761cc0

…ith the no args help

src/bound_pop.cpp: providing option to report histogram to a file

96714f9

src/pop_size.cpp: providing option to report histogram to a file

c62b649

src/load_data_for_complexity.cpp: satsifying cpplint

5976618

src/to-mr.cpp: removing this file as its only remaining functionality…

ea1ee85

… has now been included in gc_extrap with BAM input

src/moment_sequence.cpp: fixing a var shadowing earlier var, adding c…

539bc81

…onst to args for LU_determinant

src/moment_sequence.cpp: removing the ACCEPT_HANKEL variable because …

ef0dc93

…although it was used in a condition and set both true and false in different places, when it was set to false a return always happened immediately

src/continued_fraction.hpp: removing the return_degree function as it…

fd8fdd2

… was never used

Collapsing consecutive verbose conditions and factoring a big chunk o…

6b42ed7

…f verbose printing into a function from bound_pop

.cppcheck_suppress: adding a config file for cppcheck

eda26a5

src/continued_fraction.hcpp: removing an unused function

7c9f9c7

src/bam_record_utils.hpp: fixing the use of bool values in less-than …

0f896af

…comparison

src/bam_record_utils.cpp: fixing some issues from cppcheck including …

519239d

…failing to throw an exception that was constructed

src/load_data_for_complexity.cpp: removing some unused variables

6b4c49b

.github/workflows/cpplint.yml: removing the step of checking version

12c73b5

.cppcheck_suppress: adding newline before eof

e1dee37

cppcheck.yml: adding workflow for cppcheck

afd38e7

only writing histograms to files and this is separate from verbose

402a67f

Removing the unused srand with pid and time because it was never used…

d35eaf4

… in initializing the mt19937 which was generating randoms

clang-format

c1005a5

.github/workflows/cppcheck.yml: trying to find cppcheck

e4cc220

.github/workflows/cppcheck.yml: found cppcheck

dbcf158

andrewdavidsmith merged commit fb9b8e3 into master Oct 20, 2024
3 checks passed

andrewdavidsmith deleted the submodule-update branch October 20, 2024 04:37

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Several major updates #78

Several major updates #78

andrewdavidsmith commented Oct 20, 2024

Several major updates #78

Several major updates #78

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andrewdavidsmith commented Oct 20, 2024