No chromosome with 2 numbers in the output wig
Closed this issue · 18 comments
Trying to do (something that used to work one year ago) :
Didn't change the executable.
wiggletools write final.wig trim length.chromosomes.sorted.bed diff mean A.rep1.bw B.rep2.bw : C.control.bw
To explain a little bit, I compute the mean of two replicates and remove the input signal. I don't remember the trim part but this is the part that creates the error. Without the trim part , the output is fine.
In output final.wig , I have only signal for chr1 to chr9 and (chrX / chrY).
I revert back these files (A.rep1.bw B.rep2.bw C.control.bw) to wig to check if also they were empty for chr10 for example but they contain signal for chromosomes with two numbers.
awk '{ print $1}' final.wig | sort -u
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
chrY
Any ideas ?
My file with chrom length : length.chromosomes.sorted.bed diff
GL000008.2 0 209709
GL000009.2 0 201709
GL000194.1 0 191469
GL000195.1 0 182896
GL000205.2 0 185591
GL000208.1 0 92689
GL000213.1 0 164239
GL000214.1 0 137718
GL000216.2 0 176608
GL000218.1 0 161147
GL000219.1 0 179198
GL000220.1 0 161802
GL000221.1 0 155397
GL000224.1 0 179693
GL000225.1 0 211173
GL000226.1 0 15008
KI270302.1 0 2274
KI270303.1 0 1942
KI270304.1 0 2165
KI270305.1 0 1472
KI270310.1 0 1201
KI270311.1 0 12399
KI270312.1 0 998
KI270315.1 0 2276
KI270316.1 0 1444
KI270317.1 0 37690
KI270320.1 0 4416
KI270322.1 0 21476
KI270329.1 0 1040
KI270330.1 0 1652
KI270333.1 0 2699
KI270334.1 0 1368
KI270335.1 0 1048
KI270336.1 0 1026
KI270337.1 0 1121
KI270338.1 0 1428
KI270340.1 0 1428
KI270362.1 0 3530
KI270363.1 0 1803
KI270364.1 0 2855
KI270366.1 0 8320
KI270371.1 0 2805
KI270372.1 0 1650
KI270373.1 0 1451
KI270374.1 0 2656
KI270375.1 0 2378
KI270376.1 0 1136
KI270378.1 0 1048
KI270379.1 0 1045
KI270381.1 0 1930
KI270382.1 0 4215
KI270383.1 0 1750
KI270384.1 0 1658
KI270385.1 0 990
KI270386.1 0 1788
KI270387.1 0 1537
KI270388.1 0 1216
KI270389.1 0 1298
KI270390.1 0 2387
KI270391.1 0 1484
KI270392.1 0 971
KI270393.1 0 1308
KI270394.1 0 970
KI270395.1 0 1143
KI270396.1 0 1880
KI270411.1 0 2646
KI270412.1 0 1179
KI270414.1 0 2489
KI270417.1 0 2043
KI270418.1 0 2145
KI270419.1 0 1029
KI270420.1 0 2321
KI270422.1 0 1445
KI270423.1 0 981
KI270424.1 0 2140
KI270425.1 0 1884
KI270429.1 0 1361
KI270435.1 0 92983
KI270438.1 0 112505
KI270442.1 0 392061
KI270448.1 0 7992
KI270465.1 0 1774
KI270466.1 0 1233
KI270467.1 0 3920
KI270468.1 0 4055
KI270507.1 0 5353
KI270508.1 0 1951
KI270509.1 0 2318
KI270510.1 0 2415
KI270511.1 0 8127
KI270512.1 0 22689
KI270515.1 0 6361
KI270516.1 0 1300
KI270517.1 0 3253
KI270518.1 0 2186
KI270519.1 0 138126
KI270521.1 0 7642
KI270522.1 0 5674
KI270528.1 0 2983
KI270529.1 0 1899
KI270530.1 0 2168
KI270538.1 0 91309
KI270539.1 0 993
KI270544.1 0 1202
KI270548.1 0 1599
KI270579.1 0 31033
KI270580.1 0 1553
KI270581.1 0 7046
KI270582.1 0 6504
KI270583.1 0 1400
KI270584.1 0 4513
KI270587.1 0 2969
KI270588.1 0 6158
KI270589.1 0 44474
KI270590.1 0 4685
KI270591.1 0 5796
KI270593.1 0 3041
KI270706.1 0 175055
KI270707.1 0 32032
KI270708.1 0 127682
KI270709.1 0 66860
KI270710.1 0 40176
KI270711.1 0 42210
KI270712.1 0 176043
KI270713.1 0 40745
KI270714.1 0 41717
KI270715.1 0 161471
KI270716.1 0 153799
KI270717.1 0 40062
KI270718.1 0 38054
KI270719.1 0 176845
KI270720.1 0 39050
KI270721.1 0 100316
KI270722.1 0 194050
KI270723.1 0 38115
KI270724.1 0 39555
KI270725.1 0 172810
KI270726.1 0 43739
KI270727.1 0 448248
KI270728.1 0 1872759
KI270729.1 0 280839
KI270730.1 0 112551
KI270731.1 0 150754
KI270732.1 0 41543
KI270733.1 0 179772
KI270734.1 0 165050
KI270735.1 0 42811
KI270736.1 0 181920
KI270737.1 0 103838
KI270738.1 0 99375
KI270739.1 0 73985
KI270740.1 0 37240
KI270741.1 0 157432
KI270742.1 0 186739
KI270743.1 0 210658
KI270744.1 0 168472
KI270745.1 0 41891
KI270746.1 0 66486
KI270747.1 0 198735
KI270748.1 0 93321
KI270749.1 0 158759
KI270750.1 0 148850
KI270751.1 0 150742
KI270752.1 0 27745
KI270753.1 0 62944
KI270754.1 0 40191
KI270755.1 0 36723
KI270756.1 0 79590
KI270757.1 0 71251
chr1 0 248956422
chr10 0 133797422
chr11 0 135086622
chr12 0 133275309
chr13 0 114364328
chr14 0 107043718
chr15 0 101991189
chr16 0 90338345
chr17 0 83257441
chr18 0 80373285
chr19 0 58617616
chr2 0 242193529
chr20 0 64444167
chr21 0 46709983
chr22 0 50818468
chr3 0 198295559
chr4 0 190214555
chr5 0 181538259
chr6 0 170805979
chr7 0 159345973
chr8 0 145138636
chr9 0 138394717
chrM 0 16569
chrX 0 156040895
chrY 0 57227415
Hello @LucoLab ,
Please disregard my previous suggestion (deleted from this thread to reduce confusion), your chromosome length file was indeed sorted alphabetically (d'oh!).
Nonetheless, it feels strongly like a sorting issue. If the chromosomes are not visited in the same order across both files, trouble will ensue.
What happens if you do:
wiggletools write_bg - diff mean A.rep1.bw B.rep2.bw : C.control.bw | cut -f1 | uniq
The order of appearance of the chromosomes should correspond to that of the chromosome length file.
Cheers,
Daniel
Ok they are not in the same order as length.chromosomes.sorted.bed diff :
wiggletools write_bg - diff mean A.rep1.bw B.rep2.bw : C.control.bw | cut -f1 | uniq
So I will try to sort length.chromosomes.sorted.bed as the order given by your command.
The wig where created by bamCoverage from deeptools(3.3.1) and it's possible we update this tool recently. So they may have made some changes in their sort process. (or I may have change the order of length.chromosomes file..)
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
chrM
GL000008.2
GL000009.2
GL000194.1
GL000195.1
GL000205.2
GL000208.1
GL000213.1
GL000214.1
GL000216.2
GL000218.1
GL000219.1
GL000220.1
GL000221.1
GL000224.1
GL000225.1
GL000226.1
KI270302.1
KI270303.1
KI270304.1
KI270305.1
KI270310.1
KI270311.1
KI270312.1
KI270315.1
KI270316.1
KI270317.1
KI270320.1
KI270322.1
KI270329.1
KI270330.1
KI270333.1
KI270334.1
KI270335.1
KI270336.1
KI270337.1
KI270338.1
KI270340.1
KI270362.1
KI270363.1
KI270364.1
KI270366.1
KI270371.1
KI270372.1
KI270373.1
KI270374.1
KI270375.1
KI270376.1
KI270378.1
KI270379.1
KI270381.1
KI270382.1
KI270383.1
KI270384.1
KI270385.1
KI270386.1
KI270387.1
KI270388.1
KI270389.1
KI270390.1
KI270391.1
KI270392.1
KI270393.1
KI270394.1
KI270395.1
KI270396.1
KI270411.1
KI270412.1
KI270414.1
KI270417.1
KI270418.1
KI270419.1
KI270420.1
KI270422.1
KI270423.1
KI270424.1
KI270425.1
KI270429.1
KI270435.1
KI270438.1
KI270442.1
KI270448.1
KI270465.1
KI270466.1
KI270467.1
KI270468.1
KI270507.1
KI270508.1
KI270509.1
KI270510.1
KI270511.1
KI270512.1
KI270515.1
KI270516.1
KI270517.1
KI270518.1
KI270519.1
KI270521.1
KI270522.1
KI270528.1
KI270529.1
KI270530.1
KI270538.1
KI270539.1
KI270544.1
KI270548.1
KI270579.1
KI270580.1
KI270581.1
KI270582.1
KI270583.1
KI270584.1
KI270587.1
KI270588.1
KI270589.1
KI270590.1
KI270591.1
KI270593.1
KI270706.1
KI270707.1
KI270708.1
KI270709.1
KI270710.1
KI270711.1
KI270712.1
KI270713.1
KI270714.1
KI270715.1
KI270716.1
KI270717.1
KI270718.1
KI270719.1
KI270720.1
KI270721.1
KI270722.1
KI270723.1
KI270724.1
KI270725.1
KI270726.1
KI270727.1
KI270728.1
KI270729.1
KI270730.1
KI270731.1
KI270732.1
KI270733.1
KI270734.1
KI270735.1
KI270736.1
KI270737.1
KI270738.1
KI270739.1
KI270740.1
KI270741.1
KI270742.1
KI270743.1
KI270744.1
KI270745.1
KI270746.1
KI270747.1
KI270748.1
KI270749.1
KI270750.1
KI270751.1
KI270752.1
KI270753.1
KI270754.1
KI270755.1
KI270756.1
KI270757.1
Using a file sorted as the output of your command gives me an error :
Bed file length.chromosomes.bed is not sorted!
Position chr10:1 is before chr9:1
File used length.chromosomes.bed:
chr1 0 248956422
chr2 0 242193529
chr3 0 198295559
chr4 0 190214555
chr5 0 181538259
chr6 0 170805979
chr7 0 159345973
chr8 0 145138636
chr9 0 138394717
chr10 0 133797422
chr11 0 135086622
chr12 0 133275309
chr13 0 114364328
chr14 0 107043718
chr15 0 101991189
chr16 0 90338345
chr17 0 83257441
chr18 0 80373285
chr19 0 58617616
chr20 0 64444167
chr21 0 46709983
chr22 0 50818468
chrX 0 156040895
chrY 0 57227415
chrM 0 16569
GL000008.2 0 209709
GL000009.2 0 201709
GL000194.1 0 191469
GL000195.1 0 182896
GL000205.2 0 185591
GL000208.1 0 92689
GL000213.1 0 164239
GL000214.1 0 137718
GL000216.2 0 176608
GL000218.1 0 161147
GL000219.1 0 179198
GL000220.1 0 161802
GL000221.1 0 155397
GL000224.1 0 179693
GL000225.1 0 211173
GL000226.1 0 15008
KI270302.1 0 2274
KI270303.1 0 1942
KI270304.1 0 2165
KI270305.1 0 1472
KI270310.1 0 1201
KI270311.1 0 12399
KI270312.1 0 998
KI270315.1 0 2276
KI270316.1 0 1444
KI270317.1 0 37690
KI270320.1 0 4416
KI270322.1 0 21476
KI270329.1 0 1040
KI270330.1 0 1652
KI270333.1 0 2699
KI270334.1 0 1368
KI270335.1 0 1048
KI270336.1 0 1026
KI270337.1 0 1121
KI270338.1 0 1428
KI270340.1 0 1428
KI270362.1 0 3530
KI270363.1 0 1803
KI270364.1 0 2855
KI270366.1 0 8320
KI270371.1 0 2805
KI270372.1 0 1650
KI270373.1 0 1451
KI270374.1 0 2656
KI270375.1 0 2378
KI270376.1 0 1136
KI270378.1 0 1048
KI270379.1 0 1045
KI270381.1 0 1930
KI270382.1 0 4215
KI270383.1 0 1750
KI270384.1 0 1658
KI270385.1 0 990
KI270386.1 0 1788
KI270387.1 0 1537
KI270388.1 0 1216
KI270389.1 0 1298
KI270390.1 0 2387
KI270391.1 0 1484
KI270392.1 0 971
KI270393.1 0 1308
KI270394.1 0 970
KI270395.1 0 1143
KI270396.1 0 1880
KI270411.1 0 2646
KI270412.1 0 1179
KI270414.1 0 2489
KI270417.1 0 2043
KI270418.1 0 2145
KI270419.1 0 1029
KI270420.1 0 2321
KI270422.1 0 1445
KI270423.1 0 981
KI270424.1 0 2140
KI270425.1 0 1884
KI270429.1 0 1361
KI270435.1 0 92983
KI270438.1 0 112505
KI270442.1 0 392061
KI270448.1 0 7992
KI270465.1 0 1774
KI270466.1 0 1233
KI270467.1 0 3920
KI270468.1 0 4055
KI270507.1 0 5353
KI270508.1 0 1951
KI270509.1 0 2318
KI270510.1 0 2415
KI270511.1 0 8127
KI270512.1 0 22689
KI270515.1 0 6361
KI270516.1 0 1300
KI270517.1 0 3253
KI270518.1 0 2186
KI270519.1 0 138126
KI270521.1 0 7642
KI270522.1 0 5674
KI270528.1 0 2983
KI270529.1 0 1899
KI270530.1 0 2168
KI270538.1 0 91309
KI270539.1 0 993
KI270544.1 0 1202
KI270548.1 0 1599
KI270579.1 0 31033
KI270580.1 0 1553
KI270581.1 0 7046
KI270582.1 0 6504
KI270583.1 0 1400
KI270584.1 0 4513
KI270587.1 0 2969
KI270588.1 0 6158
KI270589.1 0 44474
KI270590.1 0 4685
KI270591.1 0 5796
KI270593.1 0 3041
KI270706.1 0 175055
KI270707.1 0 32032
KI270708.1 0 127682
KI270709.1 0 66860
KI270710.1 0 40176
KI270711.1 0 42210
KI270712.1 0 176043
KI270713.1 0 40745
KI270714.1 0 41717
KI270715.1 0 161471
KI270716.1 0 153799
KI270717.1 0 40062
KI270718.1 0 38054
KI270719.1 0 176845
KI270720.1 0 39050
KI270721.1 0 100316
KI270722.1 0 194050
KI270723.1 0 38115
KI270724.1 0 39555
KI270725.1 0 172810
KI270726.1 0 43739
KI270727.1 0 448248
KI270728.1 0 1872759
KI270729.1 0 280839
KI270730.1 0 112551
KI270731.1 0 150754
KI270732.1 0 41543
KI270733.1 0 179772
KI270734.1 0 165050
KI270735.1 0 42811
KI270736.1 0 181920
KI270737.1 0 103838
KI270738.1 0 99375
KI270739.1 0 73985
KI270740.1 0 37240
KI270741.1 0 157432
KI270742.1 0 186739
KI270743.1 0 210658
KI270744.1 0 168472
KI270745.1 0 41891
KI270746.1 0 66486
KI270747.1 0 198735
KI270748.1 0 93321
KI270749.1 0 158759
KI270750.1 0 148850
KI270751.1 0 150742
KI270752.1 0 27745
KI270753.1 0 62944
KI270754.1 0 40191
KI270755.1 0 36723
KI270756.1 0 79590
KI270757.1 0 7125
Hello again,
This probably boils down to sorting functions, which are tied to Unix locale.
To be clear: the order of chromosomes chr1, chr2, chr3... chr9, chr10... came from the wiggletools write_bg - diff mean A.rep1.bw B.rep2.bw : C.control.bw | cut -f1 | uniq command or from your wig file? Note that the bigwig files are not read in the same order as wigs.
Cheers,
Daniel
Yes they came from your command.
wiggletools write_bg - diff mean A.rep1.bw B.rep2.bw : C.control.bw | cut -f1 | uniq
Then I tried to do again with length.chromosomes.bed ordered as the result of your command.
wiggletools write final.wig trim length.chromosomes.bed diff mean A.rep1.bw B.rep2.bw : C.control.bw
It's where I have the error but it's weird because chr9 is before chr10 in length.chromosomes.bed.
Bed file length.chromosomes.bed is not sorted!
Position chr10:1 is before chr9:1
OK, so the issue is that the first command is reading the chromosomes in an arbitrary order (that used when creating the BigWig file) which is not the order expected by WiggleTools.
I'll have to correct this.
Ok thanks !
I've just pushed a commit on the master branch, could you please re-compile and give it a spin?
I'll give a try.
Hummm I tried to recompile but got some errors. Any advices to correct and go faster.
make
cd src; make -e
make[1]: Entering directory '/home/jean-philippe.villemin/bin/WiggleTools/new_version/WiggleTools-master/src'
/home/jean-philippe.villemin/bin/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I../../libBigWig -I../../htslib -D_PBGZF_USE -c bigWiggleReader.c -o bigWiggleReader.o
In file included from ../../libBigWig/bigWig.h:4:0,
from bigWiggleReader.c:16:
../../libBigWig/bigWigIO.h:5:10: fatal error: curl/curl.h: No such file or directory
#include <curl/curl.h>
^~~~~~~~~~~~~
compilation terminated.
I am on
Debian 3.16.74-1 (2019-09-24) x86_64 GNU/Linux
Previous lib are installed (from my .profile) :
export C_INCLUDE_PATH="$HOME/bin/gsl-2.3/bin/include:$HOME/bin/libBigWig/bin/include:$HOME/bin/htslib/bin/include"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/bin/libBigWig/bin/lib:$HOME/bin/gsl-2.3/bin/lib:$HOME/bin/htslib/bin/lib"
Not sure it was a good idea but I tried to install previous in my conda env but compilation is still failing due to the curl.h file.
conda install -c conda-forge gsl
conda install -c bioconda libbigwig
conda install -c anaconda curl
Hello,
Were you able to compile the libBigWig library independently in the first place?
Cheers,
Daniel
Initially a long time ago yes, I tried to re-compile with the last version from your link but with no sucess(still curl problem). In libbigwig dir :
make
/home/jean-philippe.villemin/bin/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -I. -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -c -o io.o io.c
io.c:2:10: fatal error: curl/curl.h: No such file or directory
#include <curl/curl.h>
^~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:33: io.o] Error 1
Hmm, if you installed curl with conda, I'm guessing you need to expand you C_INCLUDE_PATH and LD_LIBRARY_PATH to point to wherever conda drops headers and libs?
Yeahhh , I will look later because I need to grap the kids at school, sorry . But curl.h is on my system even at different locations so yeah my config need to be clean up. I ll tell you. But I m in coda env so it should find it after a conda install and shoul not take into account old C_INCLUDE...anyway, I might be wrong.Thanks for you time, have a good weekend.
locate curl.h
/home/jean-philippe.villemin/bin/anaconda3/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3/pkgs/libcurl-7.65.2-h20c2e04_0/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/envs/majiq_env/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/envs/outrigger-env/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/envs/python2/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/envs/r_env/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/pkgs/curl-7.52.1-0/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/pkgs/curl-7.55.1-h78862de_4/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/pkgs/curl-7.55.1-hcb0b314_2/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/pkgs/libcurl-7.61.0-h1ad7b7a_0/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/pkgs/libcurl-7.64.0-h01ee5af_0/include/curl/curl.h
/home/jean-philippe.villemin/bin/anaconda3_4.5.11/pkgs/libcurl-7.65.3-h20c2e04_0/include/curl/curl.h
/home/jean-philippe.villemin/bin/cmake-3.8.1/Utilities/cm_curl.h
/home/jean-philippe.villemin/bin/cmake-3.8.1/Utilities/cmcurl/include/curl/curl.h
/home/jean-philippe.villemin/bin/packages_R-3.3.1/include/curl/curl.h
/usr/include/curl/curl.h
Outside conda env, it's not complaining about curl but still errors (not related to missing things I think) :
cd src; make -e
make[1]: Entering directory '/home/jean-philippe.villemin/bin/WiggleTools-upgraded/src'
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c bigWiggleReader.c -o bigWiggleReader.o
bigWiggleReader.c: In function ‘BigWiggleReaderSeek’:
bigWiggleReader.c:108:14: warning: assignment discards ‘const’ qualifier from pointer target type
data->chrom = chrom;
^
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c multiplexer.c -o multiplexer.occ -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c reducers.c -o reducers.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c bedReader.c -o bedReader.o
bedReader.c: In function ‘BedReaderSeek’:
bedReader.c:95:14: warning: assignment discards ‘const’ qualifier from pointer target type
data->chrom = chrom;
^
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c bigBedReader.c -o bigBedReader.o
bigBedReader.c: In function ‘BigBedReaderSeek’:
bigBedReader.c:109:14: warning: assignment discards ‘const’ qualifier from pointer target type
data->chrom = chrom;
^
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c bamReader.c -o bamReader.o
bamReader.c: In function ‘BamReaderSeek’:
bamReader.c:227:14: warning: assignment discards ‘const’ qualifier from pointer target type
data->chrom = chrom;
^
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c apply.c -o apply.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c commandParser.c -o commandParser.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c wigWriter.c -o wigWriter.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c statistics.c -o statistics.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c unaryOps.c -o unaryOps.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c multiSet.c -o multiSet.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c setComparisons.c -o setComparisons.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c bufferedReader.c -o bufferedReader.o
bufferedReader.c: In function ‘compare_chrom_lengths’:
bufferedReader.c:188:2: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration]
return strcmp(cl_A->chrom, cl_B->chrom);
^
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c vcfReader.c -o vcfReader.o
vcfReader.c: In function ‘VcfReaderSeek’:
vcfReader.c:70:14: warning: assignment discards ‘const’ qualifier from pointer target type
data->chrom = chrom;
^
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c bcfReader.c -o bcfReader.o
bcfReader.c: In function ‘downloadBCFFile’:
bcfReader.c:53:52: warning: passing argument 2 of ‘pushValuesToBuffer’ discards ‘const’ qualifier from pointer target type
if (pushValuesToBuffer(data->bufferedReaderData, bcf_hdr_id2name(data->bcf_header, vcf_line->rid), vcf_line->pos+1, vcf_line->pos+2, 1))
^
In file included from bcfReader.c:19:0:
bufferedReader.h:30:6: note: expected ‘char *’ but argument is of type ‘const char *’
bool pushValuesToBuffer(BufferedReaderData * data, char * chrom, int start, int finish, double value);
^
bcfReader.c: In function ‘BcfReaderSeek’:
bcfReader.c:94:14: warning: assignment discards ‘const’ qualifier from pointer target type
data->chrom = chrom;
^
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c plots.c -o plots.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c mWigWriter.c -o mWigWriter.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c recycleBin.c -o recycleBin.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c fib.c -o fib.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c samReader.c -o samReader.o
samReader.c: In function ‘SamReaderSeek’:
samReader.c:186:14: warning: assignment discards ‘const’ qualifier from pointer target type
data->chrom = chrom;
^
mkdir -p ../lib
ar rcs ../lib/libwiggletools.a *.o
cc -g -Wall -O3 -std=gnu99 -I../../libBigWig -I../../htslib -D_PBGZF_USE -c wiggletools.c -o wiggletools.o
mkdir -p ../bin
cc -g -Wall -O3 -std=gnu99 -L../lib -L../../libBigWig -L../../htslib wiggletools.c -lwiggletools -l:libBigWig.a -lcurl -l:libhts.a -lgsl -lgslcblas -lz -lpthread -lm -llzma -lbz2 -o ../bin/wiggletools
/usr/bin/ld: ../lib/libwiggletools.a(wigReader.o): unrecognized relocation (0x29) in section `.text.WiggleReaderSeek'
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:15: ../bin/wiggletools] Error 1
make[1]: Leaving directory '/home/jean-philippe.villemin/bin/WiggleTools-upgraded/src'
make: *** [Makefile:7: Wiggletools] Error 2
That's new, I've never seen such a linker error in many years of C programming!
Apparently it's due to multiple version of ld being used.
Let's start with the basics, could you please do make clean; make ?
(You can ignore the warnings about const)
Ok it worked I think. Thanks. The executable is created. I will do some test now using length.chromosomes.bed.
Ace! Thanks for the rapid responses and detailed report, much appreciated!