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View Code? Open in Web Editor NEWa lightweight bam file depth statistical tool
License: Other
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rmdupdep includes low quality reads below the threshold
Both the documentation here: https://github.com/shiquan/bamdst/blob/master/bamdst.c#L435
- rmdup depth remove duplication, and only calculate the reads which\n
are primary mapped and mapQ >= cutoff_mapQ (default 20)\n\
and the internal code comment here: https://github.com/shiquan/bamdst/blob/master/bamdst.c#L155
// clean depth, rmdup, mapQ > 20, primary hit
Indicate that the intention is that low quality reads should be excluded, but the code here:
https://github.com/shiquan/bamdst/blob/master/bamdst.c#L853
doesn't appear to be enforcing that, so that columns is including low quality reads in the coverage calculations.
I'd like to know bamdst how to handle overlapping pair-end reads
I'd like to know bamdst how to handle overlapping pair-end reads when counting average depth. For example, I have paired read like the one below; will its overlapping region be counted once or twice?
exit issue
The EXIT_CODE has always been 1, but the result seems like correct.
It's really a chip in porridge, but can be confused somehow.
I hope this can be fixed in the future.
Is the Merging of bed files with respect to strand?
Hi,
I have some gene annotations in bed format, and I would like to calculate the reads coverage use your wonderful bamdst. But since it mandatorily merged region files first, I would split my bed file into several non overlap files. So I was wondering that does the merging in bamdst consider strand information?
best wishes
songtao gui
Coverage difference between bamdst and gatk DepthOfCoverage
Does bamdst remove duplicates reads automatically? I first used the "time picard MarkDuplicates REMOVE_DUPLICATES=true" function and calculate the coverage using "gatk DepthOfCoverage" based on removed duplicated bam file. The I used bamdst to calculate the coverage based on unremoved duplicated bam file, because I thought bamdst has the function of remove duplicates. However, bamdst calculated a much more higher coverage(100X) than gatk. How could this happen?
make error
hi，When I installed bamdst，I get this error:
$ make
rm -fr gmon.out *.o a.out *.exe *.dSYM bamdst *~ *.a target.dep *.plot *.report *.tsv.gz uncover.bed
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_close’:
bgzf.c:435:18: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
435 | int ret, count, block_length;
| ^~~~~
bgzf.c: In function ‘bgzf_check_EOF’:
bgzf.c:59:34: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
59 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp)
| ^~~~~~~~~~~~~~~~~~~~~~
bgzf.c:467:9: note: in expansion of macro ‘_bgzf_read’
467 | _bgzf_read(fp->fp, buf, 28);
| ^~~~~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam.c -o bam.o
In file included from /usr/include/string.h:495,
from samlib/bam.h:47,
from samlib/bam.c:5:
In function ‘strncpy’,
inlined from ‘bam_header_write’ at samlib/bam.c:128:2:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_import.c -o bam_import.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_index.c -o bam_index.o
samlib/bam_index.c: In function ‘bam_index_core’:
samlib/bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow]
178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
| ^~~~~~~~
samlib/bam_index.c: In function ‘bam_index_load_core’:
samlib/bam_index.c:335:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
335 | fread(magic, 1, 4, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
samlib/bam_index.c:342:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
342 | fread(&idx->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~
samlib/bam_index.c:355:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
355 | fread(&size, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
samlib/bam_index.c:358:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
358 | fread(&key, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~
samlib/bam_index.c:362:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
362 | fread(&p->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~
samlib/bam_index.c:366:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
366 | fread(p->list, 16, p->n, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
samlib/bam_index.c:376:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
376 | fread(&index2->n, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
samlib/bam_index.c:380:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
380 | fread(index2->offset, index2->n, 8, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/sam_header.c -o sam_header.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. bedutil.c -o bedutil.o
bedutil.c: In function ‘regcore_uniq’:
bedutil.c:256:12: warning: variable ‘lastbeg’ set but not used [-Wunused-but-set-variable]
256 | uint32_t lastbeg = 0;
| ^~~~~~~
At top level:
bedutil.c:589:13: warning: ‘bed_view’ defined but not used [-Wunused-function]
589 | static void bed_view(regHash_t *reghash, char *reg)
| ^~~~~~~~
bedutil.c:180:13: warning: ‘reg_destroy’ defined but not used [-Wunused-function]
180 | static void reg_destroy(bedreglist_t *reg, bedvoid_destroy func)
| ^~~~~~~~~~~
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. commons.c -o commons.o
commons.c:3:13: warning: ‘stderr_print’ defined but not used [-Wunused-function]
3 | static void stderr_print(char *format, ...)
| ^~~~~~~~~~~~
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o bam_index.o sam_header.o bedutil.o commons.o
ar: u' modifier ignored since D' is the default (see `U')
gcc -g -Wall -O2 -o bamdst bamdst.c -L. -Isamlib/ -I. -lm -lbam -lz
bamdst.c: In function ‘init_loopbams_parameters’:
bamdst.c:663:17: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
663 | if (outdir) chdir(outdir);
| ^~~~~~~~~~~~~
bamdst.c: In function ‘write_unover_file’:
bamdst.c:821:17: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
821 | if (outdir) chdir(outdir);
| ^~~~~~~~~~~~~
bamdst.c: In function ‘load_bamfiles’:
bamdst.c:837:17: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
837 | if (outdir) chdir(outdir); // FIXME: if there is no such dir?
| ^~~~~~~~~~~~~
bamdst.c: In function ‘print_report’:
bamdst.c:1064:17: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1064 | if (outdir) chdir(outdir);
| ^~~~~~~~~~~~~
At top level:
bamdst.c:78:18: warning: ‘WINDOW_SIZE’ defined but not used [-Wunused-const-variable=]
78 | static const int WINDOW_SIZE = 102400;
| ^~~~~~~~~~~
mapped reads
Hi,
why mapped reads count differ greatly from the result of samtools view -c -F 4 *.bam. In bamdst, how to get mapped reads?
best regards
Li'anLin
make error
hi，When I installed bamdst，I get this error:
$ make
rm -fr gmon.out *.o a.out *.exe *.dSYM bamdst *~ *.a target.dep *.plot *.report *.tsv.gz uncover.bed
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. bgzf.c -o bgzf.o
In file included from bgzf.c:31:0:
bgzf.h:33:10: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^~~~~~~~
compilation terminated.
make: *** [Makefile:29: bgzf.o] Error 1
I check the /usr/include,the zlib.h is exist.How can I solve this problem？
how to use MapQ to filter read at target average depth counts (rmdup) ?
HI,
I got a question .
If I set -q 10, it means if the read mapQ is less than 10, then this read won't count to calculate target average detph (rmdup) ??
am I right ?
thank you !
Multi-genomes
How can I do to get the final report of multi-genomes? Cause I got many bins(MAGs) within several contigs after metabat ,and I want to know the mapping ratio of each MAG. However, the fraction of mapped reads in the coverage-report.txt total ratio, so how can I do to get the ratio of each MAG through one process of blast.
what each column of *.plot means
Hi shiquan, I want to use the plot files, but I don't know the meaning of each column in *.plot ,can you explain it. And do you plan to add a tool to generate plottings from the *.plot files directly.Thanks!
invalid BAM binary header (this is not a BAM file) using bamdst.
Hi,
I am new using bamdst,and I have a question.When I excute it ,it reported this below,
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Segmentation fault (core dumped)
Any advice? Thanks.
How to use multiple args in '--cutoffdepth'
like --cutoffdepth 500, 750, 1000
seems bamdst can only recognize the first number
specifying more than one --cutoffdepth value
Hi Shiquan!
I am trying to get many coverage for a BAM file. In Bamdst tool we can do this by specifying --cutoffdepth parameter, but I need to get all these coverage in a single coverage.report. How can I get this?
I tried below command but it's giving default coverage such as 0x, 4x, 10x, 30x ,100x along with first specified --cutoffdepth value "50x".
/home//softwares/bamdst-master/bamdst -p /home/packages/SureSelect_Human_All_Exon_V5+UTRs_S04380219_Aglilent/S04380219_Covered.bed -o /home//trial/bam_stat_trial /home/trial.sorted.bam --cutoffdepth 50,40,20
Please help.
Thank you
What is the meaning of each row.
Hi, I have a question about the output file: coverage.report,
some row confused me and
can I have a file which explain each row stand for?
Many thanks.
How to change the name of output file
It's hard for me to figure out how to change the name of the output file with the current option. Do you have any good suggestions? Thanks!
BUG: supplementary mapping is used for reads counting
It seems that bamdst over counting the reads number when there's some supplementary mapping reads in the bam file.
Supplementary reads make some sense for target coverage, but it should not be over counting for "total reads" or "target reads".
请问使用您的软件，如何引用？
我没能找到bamdst的原始文献，所以请问我应该如何引用您的软件呢？
question about long reads
hello,
I wonder if bamdst can perform statistics on aligned BAM files containing long reads, such as BAM files from PacBio.
Looking forward to your reply.
Thanks.
error 404 Issue installing private repos with devtools
If I follow the installation instructions using install_github("shiquan/bamdst") I get:
install_github("shiquan/bamdst")
Error: Failed to install 'unknown package' from GitHub:
HTTP error 404.
Not Found
Did you spell the repo owner (shiquan) and repo name (bamdst) correctly?
- If spelling is correct, check that you have the required permissions to access the repo.
However, the installation succeeded when I tried another: install_github("tidyverse/ggplot2")
Anyone could have some advice please?
Segmentation fault (core dumped)
Hi shiquan:
When the following simple script was executed, It crashed and threw Segmentation fault (core dumped).
/opt/bio/bamdst/bamdst -p genome.bed -o sampleA_state sampleA.bam I used the Linux Distribution: openSUSE 15.3
Is there a bug in bamdst? How can I fix it?
Wish your comments, Thanks!
[Target] Coverage (>0x) 100.00% but uncover.bed is not umpty
Hi,
i am confused about the workout, coverage.report file shows [Target] Coverage (>0x) 100.00% but uncover.bed shows 72 point. whether bam cover the full bed.
Thanks!
Memory Bugs
I met a problem like this:
@@ ERROR ABORT @@
[NeedMEM] trying to allocate 565656160 bytes (limits: 500000000)
And how to deal with it?
Suggestion - making a bioconda recipe
Hi @shiquan
Thanks for the great tool - I would suggest making this into a Bioconda recipe and having this installable/available via Bioconda - something similar to how csvtk is in bioconda - https://bioinf.shenwei.me/csvtk/download/#method-2-install-via-conda-latest-stable-version
Just a suggestion - it would be a great utility via bioconda
Thanks
how to accelerate the software bamdst
hello, thanks for your Outstanding software，
but I wander is there someway to accelerate the software？ I have about 1000 samples to do
and why it can't support CRAM format
Installation Error
Hi there, when I tried to install bamdst, I got a lot of warnings:
rm -fr gmon.out *.o a.out *.exe *.dSYM bamdst *~ *.a target.dep *.plot *.report *.tsv.gz uncover.bed
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. bgzf.c -o bgzf.o
bgzf.c:80:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./khash.h:601:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:215:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_clear##name(kh##name##_t *h...
^
:93:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_aux.c -o bam_aux.o
samlib/bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, int)
^
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:215:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_clear##name(kh##name##_t *h...
^
:88:1: note: expanded from here
kh_clear_s
^
samlib/bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:341:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_del##name(kh##name##_t *h, khint_t x...
^
:102:1: note: expanded from here
kh_del_s
^
samlib/bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]
KHASH_MAP_INIT_STR(r2l, str_p)
^
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:204:23: note: expanded from macro '_KHASH_IMPL'
SCOPE kh##name##t *kh_init##name(void) ...
^
:109:1: note: expanded from here
kh_init_r2l
^
samlib/bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l'
[-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:207:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_destroy##name(kh##name##_t *h...
^
:114:1: note: expanded from here
kh_destroy_r2l
^
samlib/bam_aux.c:6:1: warning: unused function 'kh_clear_r2l'
[-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:215:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_clear##name(kh##name##_t *h...
^
:117:1: note: expanded from here
kh_clear_r2l
^
samlib/bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:222:16: note: expanded from macro 'KHASH_IMPL'
SCOPE khint_t kh_get##name(const kh##name##_t *h, khkey_t key...
^
:120:1: note: expanded from here
kh_get_r2l
^
samlib/bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:299:16: note: expanded from macro 'KHASH_IMPL'
SCOPE khint_t kh_put##name(kh##name##_t *h, khkey_t key, int *ret)
^
:126:1: note: expanded from here
kh_put_r2l
^
samlib/bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:341:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_del##name(kh##name##_t *h, khint_t x...
^
:131:1: note: expanded from here
kh_del_r2l
^
8 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam.c -o bam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_import.c -o bam_import.o
samlib/bam_import.c:18:1: warning: unused function 'kh_clear_ref'
[-Wunused-function]
KHASH_MAP_INIT_STR(ref, uint64_t)
^
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:215:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_clear##name(kh##name##_t *h...
^
:99:1: note: expanded from here
kh_clear_ref
^
samlib/bam_import.c:18:1: warning: unused function 'kh_get_ref'
[-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:222:16: note: expanded from macro 'KHASH_IMPL'
SCOPE khint_t kh_get##name(const kh##name##_t *h, khkey_t key...
^
:102:1: note: expanded from here
kh_get_ref
^
samlib/bam_import.c:18:1: warning: unused function 'kh_del_ref'
[-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:341:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_del##name(kh##name##_t *h, khint_t x...
^
:113:1: note: expanded from here
kh_del_ref
^
3 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_index.c -o bam_index.o
samlib/bam_index.c:64:1: warning: unused function 'kh_clear_i'
[-Wunused-function]
KHASH_MAP_INIT_INT(i, bam_binlist_t)
^
./khash.h:586:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:215:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_clear##name(kh##name##_t *h...
^
:103:1: note: expanded from here
kh_clear_i
^
samlib/bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]
./khash.h:586:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:341:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_del##name(kh##name##_t *h, khint_t x...
^
:117:1: note: expanded from here
kh_del_i
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/sam_header.c -o sam_header.o
samlib/sam_header.c:9:1: warning: unused function 'kh_clear_str'
[-Wunused-function]
KHASH_MAP_INIT_STR(str, const char *)
^
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:215:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_clear##name(kh##name##_t *h...
^
:569:1: note: expanded from here
kh_clear_str
^
samlib/sam_header.c:9:1: warning: unused function 'kh_del_str'
[-Wunused-function]
./khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
^
./khash.h:358:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map...
^
./khash.h:355:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_fu...
^
./khash.h:341:13: note: expanded from macro 'KHASH_IMPL'
SCOPE void kh_del##name(kh##name##_t *h, khint_t x...
^
:583:1: note: expanded from here
kh_del_str
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. bedutil.c -o bedutil.o
bedutil.c:178:13: warning: unused function 'reg_destroy' [-Wunused-function]
static void reg_destroy(bedreglist_t *reg, bedvoid_destroy func)
^
bedutil.c:584:13: warning: unused function 'bed_view' [-Wunused-function]
static void bed_view(regHash_t *reghash, char *reg)
^
2 warnings generated.
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. commons.c -o commons.o
commons.c:3:13: warning: unused function 'stderr_print' [-Wunused-function]
static void stderr_print(char *format, ...)
^
1 warning generated.
.../envs/wes/bin/x86_64-apple-darwin13.4.0-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o bam_index.o sam_header.o bedutil.o commons.o
.../envs/wes/bin/x86_64-apple-darwin13.4.0-ranlib: object: libbam.a(bgzf.o) malformed object (unknown load command 1)
.../envs/wes/bin/x86_64-apple-darwin13.4.0-ar: internal ranlib command failed
make: *** [Makefile:23: libbam.a] Error 1
I don't know how to fix this problem, I hope you can provide some suggestions. Thanks！
multithreading support
Can this program add support for multithreading to speed up analysis，The format is similar to --thread 4
License?
This looks like a cool tool, but I'm unsure what license it's made available under. Some of the C files contain headers with Broad or BGI copyrights and MIT licenses, but others have no headers.
Could you make the license explicit by creating a LICENSE file or some other license statement (after reviewing all the included code to make sure it's compatible, of course).
Thanks!
Error ocurrus when use bamdst to stat WGS bam file
Hi, when I use bamdst to stat WGS file, the output file depth.tsv.gz just has the first chrosome result in the region file, and the task is stoped with no error information.How to slove it?
the target region:
chr1 1 254717395
chr2 1 242636919
chr3 1 199957529
chr4 1 191432471
chr5 1 183988138
chr6 1 171967578
chr7 1 158872745
chr8 1 145796002
chr9 1 137877317
chr10 1 134863434
chr11 1 135971833
chr12 1 133770623
chr13 1 105970862
chr14 1 98522907
chr15 1 94829848
chr16 1 90698698
chr17 1 83813795
chr18 1 80489117
chr19 1 62832331
chr20 1 66744663
chr21 1 45247884
chr22 1 50276510
chrX 1 157365100
chrY 1 65593761
chrM 1 16571
the run command：
bamdst -p /ref/CN1.chr.region -1 -o /work/WGS6/ --maxdepth 10000000000 --isize 1000000000 -f 0 /work/WGS6/WGS6.sort.dup.bam
@@ ERROR ABORT @@ bam files are not properly sorted
when use as ,bamdst -p <probe.bed> -o ./ in1.bam ,the bamdst give the error: bam files are not properly sorted. Could anyone help me ?
make warning
Hi @shiquan ,
I came across a warning when I make this software:
$ make
make: Warning: File 'Makefile' has modification time 585 s in the future
rm -fr gmon.out *.o a.out *.exe *.dSYM bamdst *~ *.a target.dep *.plot *.report *.tsv.gz uncover.bed
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_close’:
bgzf.c:435:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
int ret, count, block_length;
^
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam.c -o bam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_import.c -o bam_import.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/bam_index.c -o bam_index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. samlib/sam_header.c -o sam_header.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. bedutil.c -o bedutil.o
bedutil.c: In function ‘regcore_uniq’:
bedutil.c:256:12: warning: variable ‘lastbeg’ set but not used [-Wunused-but-set-variable]
uint32_t lastbeg = 0;
^
bedutil.c: At top level:
bedutil.c:180:13: warning: ‘reg_destroy’ defined but not used [-Wunused-function]
static void reg_destroy(bedreglist_t *reg, bedvoid_destroy func)
^
bedutil.c:589:13: warning: ‘bed_view’ defined but not used [-Wunused-function]
static void bed_view(regHash_t *reghash, char *reg)
^
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE -Isamlib/ -I. commons.c -o commons.o
commons.c:3:13: warning: ‘stderr_print’ defined but not used [-Wunused-function]
static void stderr_print(char *format, ...)
^
/data/xieduo/WES_pipe/pipeline/bin/Miniconda3/envs/gatk_4.2.6.1/bin/x86_64-conda-linux-gnu-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o bam_index.o sam_header.o bedutil.o commons.o
gcc -g -Wall -O2 -o bamdst -L/home/xieduo/lib/curl-7.28.0/lib -L/home/xieduo/lib/pcre2-10.39/lib -L/home/xieduo/lib/xz-5.2.5/lib -L/home/xieduo/lib/bzip2-1.0.6/lib -L/home/xieduo/lib/zlib-1.2.11/lib -L/home/xieduo/lib/libpng-1.6.37/lib -L/home/xieduo/lib/openssl-1.1.1n/lib bamdst.c -L. -Isamlib/ -I. -lm -lbam -lz
make: warning: Clock skew detected. Your build may be incomplete.
How to solve this issue? Thank you.
Best,
Duo
AMP data whitout rmdup but different
## Files : bams/case03.tumor.bam
[Total] Raw Reads (All reads) 23207660
[Total] QC Fail reads 0
[Total] Raw Data(Mb) 2862.87
[Total] Paired Reads 23207660
[Total] Mapped Reads 23204560
[Total] Fraction of Mapped Reads 99.99%
[Total] Mapped Data(Mb) 2862.45
[Total] Fraction of Mapped Data(Mb) 99.99%
[Total] Properly paired 21198750
[Total] Fraction of Properly paired 91.34%
[Total] Read and mate paired 23203400
[Total] Fraction of Read and mate paired 99.98%
[Total] Singletons 1160
[Total] Read and mate map to diff chr 1862132
[Total] Read1 11603830
[Total] Read2 11603830
[Total] Read1(rmdup) 11602187
[Total] Read2(rmdup) 11602373
[Total] forward strand reads 11639326
[Total] backward strand reads 11565234
[Total] PCR duplicate reads 0
[Total] Fraction of PCR duplicate reads 0.00%
[Total] Map quality cutoff value 20
[Total] MapQuality above cutoff reads 23115868
[Total] Fraction of MapQ reads in all reads 99.60%
[Total] Fraction of MapQ reads in mapped reads 99.62%
[Target] Target Reads 22770967
[Target] Fraction of Target Reads in all reads 98.12%
[Target] Fraction of Target Reads in mapped reads 98.13%
[Target] Target Data(Mb) 2723.67
[Target] Target Data Rmdup(Mb) 2717.17
[Target] Fraction of Target Data in all data 95.14%
[Target] Fraction of Target Data in mapped data 95.15%
[Target] Len of region 14438
[Target] Average depth 188645.84
[Target] Average depth(rmdup) 188196.05
[Target] Coverage (>0x) 99.49%
[Target] Coverage (>=4x) 97.78%
[Target] Coverage (>=10x) 95.77%
[Target] Coverage (>=30x) 93.22%
[Target] Coverage (>=100x) 91.06%
[Target] Coverage (>=500x) 87.46%
[Target] Target Region Count 88
[Target] Region covered > 0x 88
[Target] Fraction Region covered > 0x 100.00%
[Target] Fraction Region covered >= 4x 100.00%
[Target] Fraction Region covered >= 10x 100.00%
[Target] Fraction Region covered >= 30x 100.00%
[Target] Fraction Region covered >= 100x 100.00%
[Target] Fraction Region covered (>=500x) 100.00%
[flank] flank size 200
[flank] Len of region (not include target region) 48108
[flank] Average depth 56614.38
[flank] flank Reads 22771891
[flank] Fraction of flank Reads in all reads 98.12%
[flank] Fraction of flank Reads in mapped reads 98.14%
[flank] flank Data(Mb) 2723.60
[flank] Fraction of flank Data in all data 95.14%
[flank] Fraction of flank Data in mapped data 95.15%
[flank] Coverage (>0x) 40.55%
[flank] Coverage (>=4x) 31.44%
[flank] Coverage (>=10x) 30.21%
[flank] Coverage (>=30x) 29.27%
[flank] Coverage (>=100x) 28.28%
[flank] Coverage (>=500x) 26.29%
I didn't do markdup,so [Total] PCR duplicate reads 0,but i don't know why
[Target] Average depth 188645.84
[Target] Average depth(rmdup) 188196.05
what should i do?
[NeedMEM] trying to allocate 598017592 bytes (limits: 500000000)
about the depth.tsv.gz
hello,
I want to know why the depth.tsv.gz stats depth startint with position 2 instead position 1
thanks !
bigger flank reads than expected
Hi Dr.shiquan:
I am using bamdst to calculate exom sequencing enrichment efficiency. I got the the PF(passing filter) reads on flank region is 6868603, it is greatly bigger than my expected size. bamdst command is bamdst -p S07084713_Regions.bed -f 100 -o sample sample.bam. So I recalculate it step-by-step myself. Firstly I use samtools view to count PF reads on target region:samtools view -c -F 2820 -L S07084713_Regions.bed sample.bamthe result is 10352919. Secondely I added 100bp to my bed file using awk:awk '{print $1,$2-100,$3+100}' S07084713_Regions.bed|tr ' ' '\t' >padded.bed. Then samtools view to count PF reads on target +/- 100 bp :samtools view -c -F 2820 -L padded.bed. the result is 11049703. Reads on flank region is 11049703-10352919=696784, lower one order of magnitude than bamdst result. I guess something was uncorrect in my step-by-step flow, but I do not know how to figure out.By the way, according to the bamdst output result in coverage.report, could I get enrichment efficient on target +/- 100bp by ( Target Reads+flank Reads)/Mapped Reads?
best regards
Li'anLin
Raw Reads (All reads) are a bit off
bamdst is a good tools, but it has a bit problems.
Raw Reads (All reads) is equal to the result of samtools view $bam | wc -l , not the number of fastq reads. Maybe it Ignored the supplementary alignment.So is the Raw Data(Mb)
Segmentation fault (core dumped)
Hi, I'm a newer to bamdst. This is a excellent tool. I runned the example file succefully. However, when I runned the following code:
~/software/bamdst$ /home/ug0416/software/bamdst/bamdst -p /home/ug0416/mydata/genome/hg19/hg19_bed/IDTV2.chr.bed -o /home/ug0416/software/bamdst/coverage/ /home/ug0416/mydata/04.mapping/2nd_geneseed_mapping/SCA_876_T.sorted.bam
error occurred:
Segmentation fault (core dumped)
Hope your repose! Appreciate
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