samtools 1.21
Using htslib 1.21
Copyright (C) 2024 Genome Research Ltd.
Samtools compilation details:
Features: build=configure curses=yes
CC: gcc
CPPFLAGS:
CFLAGS: -Wall -I/opt/software/libdeflate/1.21/
LDFLAGS: -L/opt/software/libdeflate/1.21/build
HTSDIR: htslib-1.21
LIBS:
CURSES_LIB: -lncursesw
HTSlib compilation details:
Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=no htscodecs=1.6.1
CC: gcc
CPPFLAGS:
CFLAGS: -Wall -I/opt/software/libdeflate/1.21/ -fvisibility=hidden
LDFLAGS: -L/opt/software/libdeflate/1.21/build -fvisibility=hidden
HTSlib URL scheme handlers present:
built-in: file, preload, data
S3 Multipart Upload: s3w+https, s3w+http, s3w
Amazon S3: s3+https, s3, s3+http
Google Cloud Storage: gs+http, gs+https, gs
libcurl: smtp, ldaps, smb, rtsp, tftp, pop3, smbs, imaps, pop3s, ftps, https, http, ftp, gopher, imap, sftp, ldap, smtps, dict, scp, telnet
crypt4gh-needed: crypt4gh
mem: mem
@HD VN:1.5 SO:queryname SS:queryname:lexicographical
> diff -y -W 250 queryname.sort.stats coordinate.sorted.txt
[...]
SN is sorted: 0 | SN is sorted: 1
[...]
# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
COV [1-1] 1 2095061 | COV [1-1] 1 36918165
COV [2-2] 2 544 | COV [2-2] 2 6339356
> COV [3-3] 3 1556677
> COV [4-4] 4 423176
> COV [5-5] 5 116074
> COV [6-6] 6 36544
> COV [7-7] 7 9756
> COV [8-8] 8 3961
> COV [9-9] 9 1559
> COV [10-10] 10 857
> COV [11-11] 11 621
> COV [12-12] 12 420
> COV [13-13] 13 1107
> COV [14-14] 14 539
> COV [15-15] 15 364
> COV [16-16] 16 95
> COV [17-17] 17 112
> COV [18-18] 18 53
> COV [19-19] 19 28
> COV [20-20] 20 42
> COV [21-21] 21 71
> COV [22-22] 22 77
> COV [23-23] 23 58
> COV [24-24] 24 44
> COV [25-25] 25 27
> COV [26-26] 26 45
> COV [27-27] 27 32
> COV [28-28] 28 45
> COV [29-29] 29 95
> COV [30-30] 30 3
> COV [31-31] 31 11
# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25t # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25t
GCD 0.0 0.007 0.000 0.000 0.000 0.000 0.000 | GCD 0.0 0.001 0.000 0.000 0.000 0.000 0.000
GCD 0.5 0.011 0.004 0.004 0.004 0.004 0.004 | GCD 0.5 0.001 0.004 0.004 0.004 0.004 0.004
GCD 20.0 0.059 0.004 0.004 0.004 0.004 0.004 | GCD 9.0 0.032 0.004 0.004 0.004 0.004 0.004
GCD 21.0 0.092 0.004 0.004 0.004 0.004 0.004 | GCD 10.0 0.047 0.004 0.004 0.004 0.004 0.004
GCD 22.0 0.165 0.004 0.004 0.004 0.004 0.004 | GCD 11.0 0.063 0.004 0.004 0.004 0.004 0.004
[...]
Are you using the latest version of samtools and HTSlib? If not, please specify.
Please describe your environment.
Linux 4.18.0-553.16.1.el8_10.x86_64x86_64Please specify the steps taken to generate the issue, the command you are running and the relevant output.
The input file is
querynamesorted:If I run
samtools statson the above file (below left) or after sorting bycoordinate(below right), I get slightly different outptus:querynamewhy does it outputsis sorted: 0?COVandGCDare only supported if sorted by coordinate; if so, shouldn't they just be omitted from the output? According to the docs:Not all sections will be reported as some depend on the data being coordinate sorted while others are only present when specific barcode tags are in use.