Falco accepts BAM/SAM files without quality scores and stability added for small inputs by andrewdavidsmith · Pull Request #138 · smithlabcode/falco

andrewdavidsmith · 2026-10-06T23:50:16Z

No description provided.

…completely in case no quals in input

…ector

… be a vector

…fers in bgzf_reader

… per-read gc content containers

…d moving gzip header inside here and changing the representation of the gzip header to an array

…ed to summarizing gc content into its own sources for better maintainability

…ing, added to_line for formatting as a line in verbose output

…off, then it now turns off do_qual_seq and do_qual_base

…d changed get_qual_size and get_qual_end to allow for files with records having empty qual strings

…ear as a single asterisk in the sam record

…ores in a bam file, which will also work for a sam file

… scores in a bam file, which will also work for a sam file

…fore doing grade, report or html for quality scores by read or base

…uals-optional

… so that quality score reporting, etc., can be avoided otherwise

…s not done because that needs quals

…g identified performance issues; this should be reverted in a subsequent refactor

…ks argument updates

… array because of profiling; this should revert after refactoring later

… adds two tile_processor objects together; should always have been done

…tiles seem to have different max read lengths

…uals-optional

…increasing the min buffer size

…re and increasing the min buffer size

…tion and function signatures to be more uniform with other reads file types

…ition and function signatures to be more uniform with other reads file types

…inition and function signatures to be more uniform with other reads file types

…nition and function signatures to be more uniform with other reads file types

…e and increasing the min buffer size

…blems on macos

andrewdavidsmith added 30 commits October 1, 2026 14:25

src/run_mode.hcpp: adding general variable for quals to turn them of …

abfa99a

…completely in case no quals in input

src/falco.cpp: adding an arg for do_quals

2ad9a44

src/bam_file.cpp: changes to reflect change of input_buffer to be a v…

2a295f5

…ector

src/fqrec.hpp: changing to_string function name for uniformity

34d0538

src/fastq_bgzf_file.cpp: changes to reflect change of input_buffer to…

d38a6ec

… be a vector

src/bgzf_reader.hcpp: changing buffers to vectors

a4fd101

src/bgzf_block.hcpp: changes reflecting the pointer to vector for buf…

e929d8b

…fers in bgzf_reader

src/falco_utils.cpp: minor refactoring functions to combine different…

db6bb92

… per-read gc content containers

src/bgzf_reader.cpp: converting buffers to vectors for convenience an…

fc24f87

…d moving gzip header inside here and changing the representation of the gzip header to an array

src/bgzf_block.hpp: fixing constructors

910a290

src/bgzf_reader.cpp: fixing type mismatch when adding to iterator

7d72ca5

src/falco_utils.cpp: adding suppression

ef17f3d

src/falco_utils.hcpp and src/falco_gc_summary.hcpp: moving code relat…

79cb2a0

…ed to summarizing gc content into its own sources for better maintainability

CMakeLists.txt and src/falco_grade.hpp: using falco_gc_summary source

7af0f37

fixing includes

1a203e4

more iwyu

493cb3d

src/file_info.hpp: added has_quals variable, changed string to to_str…

b37502e

…ing, added to_line for formatting as a line in verbose output

src/file_info.cpp: adding for to_line definition

9fe6674

src/run_mode.cpp: in logic for set_unassigned, if do_quals is turned …

ba02594

…off, then it now turns off do_qual_seq and do_qual_base

src/bamrec.hpp and src/samrec.hpp: adding has_qual friend function an…

aad3579

…d changed get_qual_size and get_qual_end to allow for files with records having empty qual strings

src/samrec.cpp: changes to allow for empty quality strings, which app…

1e24322

…ear as a single asterisk in the sam record

src/quality_score.cpp: added logic to test for presence of quality sc…

7d33c42

…ores in a bam file, which will also work for a sam file

src/quality_score.hpp: added function to test for presence of quality…

f2c307a

… scores in a bam file, which will also work for a sam file

src/results_summary.cpp: added logic to examine info for has_quals be…

ee50169

…fore doing grade, report or html for quality scores by read or base

Merge branch 'quals-optional' of github.com:smithlabcode/falco into q…

7e5b767

…uals-optional

src/falco.cpp: added logic to check if quality scores exist in a file…

b2f7f0e

… so that quality score reporting, etc., can be avoided otherwise

CMakeLists.txt: adding file_info object

d61fc91

src/run_mode.hpp: comment

1595c13

src/results_collector.hpp: if do_quals is turned off, tile analysis i…

b354106

…s not done because that needs quals

src/bamrec.cpp: removing shadowing variable

403e2c2

andrewdavidsmith added 22 commits October 3, 2026 20:03

iwyu

655bda6

CMakeLists.txt: exposing htslib headers to quality_score

c79ef64

CMakeLists.txt: fix typo

416a2b7

src/bgzf_block.hcpp: using pointer instead of iterator after profilin…

5911432

…g identified performance issues; this should be reverted in a subsequent refactor

src/fastq_bgzf_file.cpp and src/bam_file.cpp: decompression block tas…

73a33d4

…ks argument updates

src/bgzf_block.hpp: headers

d95c12c

src/bgzf_reader.hcpp: changing character vector to unique_ptr to char…

5cb9a14

… array because of profiling; this should revert after refactoring later

src/bgzf_reader.cpp: static analysis suppression

6d40749

src/tile_processor.cpp: including max_read_len into the function that…

014182f

… adds two tile_processor objects together; should always have been done

src/html.cpp: fixing an assertion that shouldn't hold when different …

fefabaf

…tiles seem to have different max read lengths

src/bam_file.cpp: adding min chunk size

49db989

src/fastq_bgzf_file.cpp: adding min chunk size

a95e08d

Merge branch 'quals-optional' of github.com:smithlabcode/falco into q…

e37575f

…uals-optional

src/bam_file.hpp: fixing a variable name in make_tasks signature and …

42f9f19

…increasing the min buffer size

src/fastq_bgzf_file.hpp: fixing a variable name in make_tasks signatu…

5a3fa51

…re and increasing the min buffer size

src/sam_file.hcpp: adding min chunk size and refactoring class defini…

9d9924e

…tion and function signatures to be more uniform with other reads file types

src/sam_stdin.hcpp: adding min chunk size and refactoring class defin…

62564db

…ition and function signatures to be more uniform with other reads file types

src/fastq_stdin.hcpp: adding min chunk size and refactoring class def…

97b060d

…inition and function signatures to be more uniform with other reads file types

src/fastq_file.hcpp: adding min chunk size and refactoring class defi…

05626d6

…nition and function signatures to be more uniform with other reads file types

src/fastq_gz_file.hcpp: fixing a variable name in make_tasks signatur…

65a68d1

…e and increasing the min buffer size

src/fastq_stdin.cpp: iwyu

855f9c3

reads files: changing type for min_chunk_size because of compiler pro…

db2eb1d

…blems on macos

andrewdavidsmith merged commit 046572c into main Oct 6, 2026
2 checks passed

andrewdavidsmith deleted the quals-optional branch October 6, 2026 23:53

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Falco accepts BAM/SAM files without quality scores and stability added for small inputs - #138

Falco accepts BAM/SAM files without quality scores and stability added for small inputs#138
andrewdavidsmith merged 52 commits into
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andrewdavidsmith commented Oct 6, 2026

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